(I suppose this could be a config option, to avoid being too big of a change for current players)

I've always found it strange that in vanilla, when you shift-click a stack from a chest into your inventory, it will prioritize your hotbar, if a slot is available. But MouseTweaks will always put the items in your inventory top-first, meaning that even if a slot is open on your hotbar, it won't go there.

This is a small QOL suggestion that would be immensely satisfying to finally fix. It bugs me every time I scroll an item, because I have to scroll it out of the chest, then shift-click it onto my hotbar.

Hmm, need to check what the shift-click logic does. Matching it here indeed seems to make sense