Option 1 (using “had”) seems very unlikely to me. The situation it describes is that you currently feel that you previously experienced and previously completed knowing. It’s made even more unlikely by the reference frame “all my life”, which is not a previously completed period for anyone speaking!
Option 2 (using “have”) places the knowing in the continuous mood, meaning it started in the past (near beginning of the speaker’s life in this case) and continues through the present.
Option 2 is appropriate for both scenarios.
In the first case (conveying automatic comfort with someone), “feel as if I have” conveys the irrealis mood to the (untrue) fact of knowing this person your entire life.
In the second case (providing qualitative impression of relationship length), “feel as if I have” is again appropriate, because it is not strictly true that you have known this person your entire life. It feels that way because it is nearly that span of time (and because before you knew them you didn’t know much of anything else anyway), but irrealis is appropriate again (for a slightly different reason).
Your reasoning is on the right track, in that "had been broken" often would be read as implying agency or intent. However, had broken is perfectly correct here. In fact, you do not go far enough: if the article had said "had been broken," most native speakers would assume that some individual had broken it. There are some definite subtleties here, however.
First, let us recall that some verbs can be both transitive and intransitive. Broke is in fact one such verb. Either a subject can break an object, or an object can break, similar to how one can eat dinner or simply eat. However, since the subject is the physical recipient of the action in the first case, it is not so easy to see.
There are two ways that this sentence could be written, with three interpretations.
The coupler had broken.
Really, this the past perfect way of saying it broke. No agency implied.
The coupler had been broken.
In most contexts, this would imply that some human had broken it.
However, in this context, it would not:
The coupler had been broken for a while.
In this case, broken is merely an adjective, not a past participle, and thus refers to a state, not an action. No intent is implied.
That said, this is Indian English, which is dialectically distinct from the version I speak, so certain rules might be a little different.
Best Answer
The rephrasing is fine, however, the first leans towards the formal stylistically.
In general, the hypothetical if clauses (if + were/had) can be replaced with the construction "had/were (subject)."
For example:
"If I had known, I would have acted sooner" -> "Had I known, I would have acted sooner" "If he were taller, he could reach the ceiling" -> "Were he taller, he could reach the ceiling"
There are stylistic issues that make some replacements sound awkward and stiff.