Both of your original conversations look fine. And yes, you can combine your responses into one. Here are some possible candidates.
For example #1:
"Yes, I have already sent that email (out) today."
"Yes, I had sent that email (out) earlier today."
For example #2:
"Yes, I have already sent that email (out) yesterday."
"Yes, I had sent that email (out) yesterday."
"Yes, I had sent that email (out) last week."
"Yes, I had sent that email (out) when I was in Japan."
NOTE: In your excerpt, there is "You CANNOT use the Present Perfect with specific time expressions such as: yesterday, . . ." <== But that is not really true. Your excerpt is an overgeneralized "rule" which is not always true. There are some conditions when past-time adjuncts (such as "yesterday") can be used in a present-perfect construction. For instance, there is a counter-example in CGEL, page 144, [13.ii.a] :
- "We've already discussed it yesterday."
ASIDE: Here is a post with some info on the present perfect construction (though, unfortunately, it probably isn't directly related to your question) : What's the meaning of this present perfect sentence?
NOTE: CGEL is the 2002 reference grammar by Huddleston and Pullum et al., The Cambridge Grammar of the English Language.
The difference is that Past Perfect serves a different purpose in the first part of the sentence (I saw him / I had seen him) than in the second (before he saw / had seen me). In the first part, it's used to establish a timeline - the "past in the past" use that most English learners are primarily familiar with - while in the second, it's used to establish the situation as unreal (in a manner similar to the third conditional - cf. "If I had seen him, I would've said hi").
So going through your sentences:
[11] "I saw him before he saw me" and [12] "I had seen him before he saw me" - You did see him, and he did see you. No unreal/hypothetical situation here. Past Perfect is optional, since you don't need it to clarify the timeline - you're already using "before". You can still use it to emphasize that it's important you saw him first, though.
[13] "I saw him before he had seen me" - You did see him, and you stipulate that he would've seen you, but he didn't (eg. because you managed to sneak out first). It's analogous to [11], but since you want to signify that he didn't see you, you dial the Simple Past back to Past Perfect.
[14] "I had seen him before he had seen me" - analogous to [13], but I'd say that in this case you're placing the entire situation in the context of a "past before the past". Eg.
I saw John a week ago, and he asked me if I was at the birthday party. I was, but I had seen him before he had seen me, so I snuck off.
As for the other examples:
Sally stopped Ted before he had a chance to reply.
You don't need Past Perfect here ("had had"), since there's no ambiguity - "stopped" already implies taking away the chance to reply. In a different sentence (eg. "Sally smirked before he had / had had a chance to reply") you might have to use Past Perfect to indicate that one action prevented the other from happening.
She left the country before she wrote / had written her thesis
I wouldn't go as far as to say Past Perfect here implies she began writing. It's really more about Simple Past here meaning that the entire process of writing the thesis to completion happened after she left the country, while Past Perfect means that - at the very least - she hasn't completed writing, and she would have if it wasn't for her leaving the country. It might mean she started writing, or that she was strongly planning to start.
Snape had struck before Harry was ready, before he had even begun to summon any force of resistance.
A literal reading implies that Harry was ready after being struck, but has never begun to summon any force of resistance - but in this case I'd say it's more about gradually putting more emphasis on how much of an interruption Snape striking Harry was.
Best Answer
I ate yesterday, simple past. I have eaten many times--cannot use this tense with specific time. Many times is not specific. I had eaten yesterday, when my friend appeared at the door. Past perfect for a completed action in the past, when some other action occurred.
They haven't written yet. Time is not specific, and one uses present perfect.
I would leave it to my British colleagues to discuss biscuits. We eat them here, but the term is not used often.
They ate two biscuits two minutes ago. Simple past with specific time.