“…Because these are special abilities with a negative effect that have nothing to do with a plentiful ammo supply”, I may not reroll those 1’s."
You get the re-rolls from Plentiful Ammo first, then look at the dice. If you had plentiful ammo and Guards crew from a T-34/85, you would get to chose which of the two abilities you used first, then use the second. After all that’s done you can then look at the results for your overheat, rapid fire, flamethrower, etc.