I'd factor trap damage into a 3-turn average, yes. I'm not sure it changes that much since offensive buffs aren't worth using over 3 turns and Aht falls back to Cross Star on turn 3, though Gafka does get Wind God Strike -> stuff that hits the center square at least. The effect on damage averages is pretty subtle, I suspect, probably less than me letting Rosch use Der Lowe which amps his damage some.
Since Marco gets his Super Heal insanely late - he didn't have it when I fought the final boss - I'm totally willing to hype Aht as the best healer for the last third of the game as far as in-game use. Super Heal is pretty darn helpful (why is money sparse for a Time Traveler who can rob timelines that never happen?), and she's got solid MT healing as well.
I probably don't allow Dreamless myself either, though not 100% sure. RH has an aftergame boss but not really an aftergame. I know I never used it, despite leveling up enough to use it when grinding for the aftergame boss. (I certainly do allow SO3 aftergame skills, on the other hand, since that's a game with a pretty long aftergame you get to use them in.) Speaking of which, you mentioned most of the scary bosses in RH not being Aht-friendly. There's some truth to this, but another exception is the Aftergame boss, if you haven't tried him yet. Aht's got MT healing, some buffing, and Traps are among the fastest ways to whittle his second form down to a manageable fight.
I recall enemies occasionally charging forward in RH (and yes, you're right that they'll do it over diagonals), but yeah, I don't really recall them ever heading to the back row. I believe you that they do, though I suspect they do that less. Moreover, and already went over this, but I found that enemy movement made Aht notably *better* in-game when it came up, so not overly inclined to hold it against her. One alternate interp - not that I advocate this - is to let people fighting Radiant Historia characters move, and even move to the back row, but not let them know where Aht placed the traps. Which makes this kind of a bad gamble as they have a 1/2 chance of blowing up unless they went first (1/2 not 2/3 since the middle-back square is guaranteed to be trapped and obviously a bad bet). These are traps, after all, and games like FE9's bridge mission don't highlight the traps for you! (Unless you're BoF Karn or the like?) I presume that RH enemies can't detect them, since they walk into them in-game!
