So, the Bosmer, as we know, tend to be shorter and have a darker skin tone than their Altmeri cousins.

What I'm wondering:

-Is this appearance associated to some sort of "divine intervention", as is the case of the Dunmer and the Orsimer? (I've never heard of anything reffering to this, but maybe it would have something to do with Y'ffre and the Green Pact..)

-Is it perhaps simply product of evolution, so to speak, and adaptation to the environment of Valenwood?

-Or is it perhaps that this is what the Altmer would look like today if they had never practiced eugenics?

They took mannish wives.

Right, but wouldn't that have left them looking like Bretons?
Or at least having the same degree of difference between Altmer-Bosmer as there is Cyrodiil-Breton?

Maybe not. Altmer are very focused on purity, while the Imperials are not. That is probably what made the Altmer/Bosmer divide so much more pronounced then the that of the Bretons and Imperials.

Divine intervention was likely at least a part of it. Words of the Clanmother has Y'ffre making Bosmer out the Ehlnofey to go alongside Azura's Khajiit.

[projectile vomit]

Shorter and Darker yes but they have wooden like skin now too.

They're reverse Bretons.
See, the Bretons are more man than elf, but the Bosmer are more elf than man.

As for your second point, I've always thought that Bretons need something to differentiate themselves from the other humans. The difference between Breton and Imperial is barely noticable. Some vaguely elven features would've been nice. If not (slightly) pointed ears, then yellowed eyes (but less so than the Altmer) or more angular features would've been nice.

It could have something with Y'ffre, but I'd put my bet more on them deviating from the anuphysique of the Aldmer by not committing genocidal-beautification-progroms.