1. Magichanged monsters (both regular and v.2) gain the same EXP/Mana as the holder, and are therefore affected by effects like the Deprave status and Felonies/Managers that the user has. Tower/Team attacks split the total EXP/Mana among its members regardless of their condition (i.e. the EXP gained by everyone will still be split equally according to the # of characters in the tower/team attack, and then multipliers (deprave/felonies) are applied individually)

2. While ally kills from capturing monsters might've been intended, I'm pretty sure there's some bug(s) regarding it nonetheless. I believe I mentioned it in another topic of yours, but I get inconsistent results when I fail to capture a unit. IIRC I get 8~12 ally kills by attempting to capture a humanoid unit (which is impossible in this game), but I have over 100 units in my base. At first I thought it was some weird interaction with my units equipped with weights (and getting resurrected after the battle), but I have since disproven that.
With that said, I don't think there's much you can do to avoid ally kills if you plan to capture a lot of monsters (especially those boosted by Prinny Ball Pirates). At best, you should only heal/revive those who can put up a fight against said monsters for any future capturing attempts, as the others will just get slaughtered again. I guess you can raise/equip all your characters so that no one dies, but that's way too much effort for no real reason. And when I say that it's because ally kills are only used to trigger the Bad Endings (which you might actually be going after), and even then you can circumvent that by removing Adell's displayed felonies (another requirement for the bad endings) using the bill to "Reincarnate to Atone for Sins".

While not related to the question, after experimenting with the weights, it seems that getting revived from capturing monsters doesn't consume the item (they are usually lost if the character equipped gets defeated during a stage).