I have had big heads mutator on and there are some moments when allies don’t have a big head and some of them do in the cutscene.
Jack only has one arm instead of 2.
But if you change the ability for the side that is missing Jack does change it when you go back but still no arm.
I have also noticed, i have played Act 1 on Inconceivable so far and progress is being done on my Seriously 5.0 achievement. Which i am guessing means even though it specifically says Insane for the achievement you possibly can unlock on Inconceivable
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Probably because Inconceivable is just a harder version of Insane so it wouldn’t make sense if it didn’t count towards Seriously.
As for the missing Jack arm bug, that’s been around for a while but I think it kinda looks funny especially when you notice it during a cutscene. Pretty sure it even happens in the customization menu sometimes.
I’m glad the achievements stack. I’ve done the serious chivo already but a few buddies haven’t so wanna replay to get all chivos at once. 
I’m glad they stack too, 
I haven’t saw the missing arm on Jack before you would have thought they would have fixed old bugs from the Campaign by now
Well the Jack bug isn’t really gamebreaking and only visual, so it seems fine that it hasn’t really been fixed.