I've read a ton of Spuffy fic, and I can honestly say that I have NEVER read a fic "explaining" the AR in Seeing Red. It's seen as indefensible, I'd say. I have seen fic that changes things so it doesn't happen, some which have Spike going for the soul for other reasons, some which skip the soul thing entirely. Another way I've seen it handled is that Buffy explains/downplays it, but in those cases Spike generally tells her she's wrong ("you like men who hurt you").

That's not to say that there aren't other common problems with Spuffy fic, the most egregious of which is that everybody but Spike is evil. I think Spike would be insulted, myself.

As for Bangel, if a person ships that through all time there are plenty of fixes that could be applied at strategic moments, but as Angel seems to think that his decision-making is noble and correct, his shippers do, too. I prefer petty, jealous, blinded by hubris Angel, myself. ;-)