Sentence structure is totally independent of its meaning, or the thing it wants to convey. Your confusion greatly roots on the fact that you are so concerned on the actual meaning of the sentence rather than the structure itself.
But let me demonstrate why "because" falls into subordinating conjunction category:
In your example
He passed because he was intelligent.
Note that there is only one line of thought here: The mere fact that he was intelligent made him pass the exam. In other words, you are basically saying that being intelligent is a cause for him passing the test.
On the other hand
He was intelligent therefore he passed the exam
Note that there are two separate states here: first, the fact that he was intelligent; and second, the fact that he passed the exam. What "therefore" did is to combine these two separate facts in order to make an inference.
Any expectation of a comma in the examples of the OP has very little to do with the subordinate clauses' restrictiveness, but rather, as the OP suggested, with an interruption of their natural flow. When leading a sentence with a subordinate clause, the comma does not force a "parenthetical / non-restrictive" interpretation. Simply, compare the meaning of two sentences:
- If you work hard, you get rewarded.
- You get rewarded if you work hard.
None of the embedded phrases in the examples were relative clauses, so the concern of imposing a non-restrictive interpretation is irrelevant. In every case, the embedding did put the interrupting phrases in a parenthetical position--even if they are considered "essential" to the meaning of the sentences.
The reference to section 6.32 of The Chicago Manual of Style 16th edition established a legitimate exception to a general rule of commas. If omitting an appropriate comma creates no ambiguity, omitting it becomes a matter of style opinion rather than grammar. Moreover, if we believe an appropriate comma introduces ambiguity, our best solution is to recast the sentence to remove ambiguity.
Considering the options for each example:
1) This is the country where[,] if you work hard, you get rewarded.
(relative clause)
The relative clause is where you get rewarded, and the comma is appropriate, because the embedded conditional phrase, if you work hard, interrupts the natural flow of the clause. The conflict between the locative where and the conditional if might be manageable enough, but many would be more comfortable with the extra comma. If the sentence had been written: This is the country where you get rewarded if you work hard, certainly no commas would be needed.
2) We need to talk because[,] if we don't, we will be in trouble.
(adverbial clause)
The adverbial clause is because we will be in trouble, and the comma is appropriate, because the embedded conditional phrase, if we don't, interrupts the natural flow of the clause. With such minuscule conflict between because and if, there is very little risk of confusion in omitting the comma. If the sentence had been written: We need to talk because we will be in trouble if we don't, certainly no commas would be needed.
3) London is where[,] when I was young, I used to live. (noun clause)
The predicative is where I used to live, and the comma would be appropriate, because the embedded adverbial phrase, when I was young, interrupts the natural flow of the clause. The locative where and the temporal when are nearly irreconcilable and should probably be separated by a comma. If the sentence had been written: London is where I used to live when I was young, certainly no commas would be needed.
4) Give me a call if[,] when you are at the station, it rains.
(adverbial clause)
The conditional clause is if it rains, and the comma is appropriate, because the embedded adverbial phrase, when you are at the station, interrupts the natural flow of the clause. The conditional if and the temporal when seem to be in deep conflict and would work better with a comma between them. If the sentence had been written: Give me a call if it rains when you are at the station, certainly no commas would be needed. The slight ambiguity could easily be eliminated by recasting the sentence to communicate the true intentions of the imperative.
5) It is useful when[,] if it rains, you have an umbrella. (awkward
adverbial clause)
The awkward adverbial clause is when you have an umbrella, and the comma is appropriate, because the embedded conditional phrase, if it rains, interrupts the natural flow of the clause. This construction is awkward with or without the comma, but would probably be less confusing with the extra comma. If the sentence had been written: It is useful when you have an umbrella if it rains, certainly no commas would be needed. The overall awkwardness still suggest a need to recast the sentence.
6) She is the person who[,] if she is faced with difficulties, can
handle them very well. (relative clause)
The relative clause is who can handle them very well, and the comma is appropriate, because the embedded conditional phrase, if she is faced with difficulties, interrupts the natural flow of the clause. The conflict between the relative who and the conditional if might be manageable without a comma, but many would find it less confusing to see the comma. If the sentence had been written: She is the person who can handle difficulties very well if she is faced with them, certainly no commas would be needed.
7) He said that[,] if all goes well, he will call. (noun clause)
The noun clause is that he will call, and the comma is appropriate, because the embedded conditional phrase, if all goes well, interrupts the natural flow of the clause. The conditional in the context of reported speech is the least awkward of the seven examples and fits the exception of The Chicago Manual of Style perfectly. If the sentence had been written: He said that he will call if all goes well, certainly no commas would be needed.
Conclusion:
The ultimate purpose of commas is clarity. Use one if it makes things more clear. Leave it out if it makes things less clear, and in my humble opinion: when in doubt, leave it out. Most importantly, recasting the way we put phrases together can eliminate most of our comma confusion.
Best Answer
Okay. It's fine-ish.
The tense seems a bit odd. You are talking about a possibility for the future (relative to now?) and of a hope in the past.
That's not wrong. It would make sense for example if someone had just told you (today) that there was a forecast of a strong chance of rain. The rain remains just a future possibility, but the hoping was done in the past, so all the tenses work logically.
It's just not a very likely combination of tenses, so standing on its own, without the context of such a forecast, it strikes me as odd, where it wouldn't just after such a forecast or some other reason for the unusual tense combination.
So let's change the tenses just so I'm no longer distracted by that!
Can I follow that? Yes.
Is my understanding of if what you wanted it to be? I'm pretty confident it is.
Do I at any point get tripped up, and have to mentally backtrack to understand you? No.
Can I see any grammatical problems? The first comma isn't wrong, but isn't necessary either, and I think you'd be better of without it, but I don't see any problems.
Can you start a sentence with two subordinating conjunctions? I'd say "yes" as a general point of theory, and I'd accept the above as evidence to back it up.
Is it a good sentence? Ah…
It takes me a while to get to your point.
Now, that's not in a terrible way. I don't get half-way through your sentence, realise I misinterpreted a clause and have to go back and start again.
But it's generally not a good thing either. There's a lot of build-up to just the hope of a sunny day.
But it's not always a bad thing.
It happens with any Because sentence, and the if adds to the effect. Consider:
Here the fact that putting the subordinate clause first leads us along for a bit before we get to the main clause is the whole reason this song works.
Your "Because if" structure increases the "leading along" quality, but the pay-off doesn't seem to be worth it.
And of course example sentences are rarely those with the best punch. (It's hard enough to think of a good sentence when writing, or a valid example when examining grammar, so doing both together is really tough). The actual form of "Because if…" I'd say is fine, I'd just better get something after it's done leading me through the subordinate clause.