Super Robot Wars, which I've Let's Sperged here, has some goofy examples of atypical game rewards/punishments.
Whenever they cover Gundam SEED/SEED Destiny's plot, they tend to mess with your head.
In SRW Alpha 3, the character Mu La Flaga, unlike canon, doesn't have to die. Simply don't deploy him in the unit he died in, and he lives to the end of the game, with cutscenes and everything taking into account his survival. The game follows canon fairly loyally otherwise, so most players either deploy him or expect the game to force deploy him and kill him off if they don't but it doesn't happen.
SRW J flips this around and kills him off automatically despite no real reason why he should have to die, even though they actually let more people live than in SRW Alpha 3's retread of the SEED plot.
SRW Z has some weird requirements for a true canon route that require doing strange things when covering Gundam SEED Destiny.
In one level, to qualify for this bonus route, you have to shoot down Kira Yamato from that show, but he's an ally (and was NOT shot down during the part of the show that stage retreads), so the game shouldn't let you kill him by default. You have to spam MAP weapons, which hit friends and foes indiscriminately, until they kill him off, and the game ordinarily encourages NOT doing this to allies, you just kill them off for no good reason doing this.
It's counter-intuitive especially because the true canon route pretty much rewrites GSD to be way less stupid in terms of plot, but you have to do strange things like mentioned above to throw the usual plot off the rails to get it.
SRW MX is also kinda goofy when covering the anime of RahXephon. Ordinarily, SRW let's you save people who should otherwise die in some horrible fashion and subvert their deaths, and through most of the game, most the crappier parts of that show are avoided or toned down, but then one level forces the PLAYER to reenact a death scene from the show, even forcing you to pull the trigger for a character's death, things SRW usually averts in one way or another.