Let Special Bags to Exclude other items types
Put Invisible bags at the bottom tabs, crafting at the second to last tab and normal bags at the top, then you don’t have this problem… There’s no reason you would need invisible bags at the top of your inventory, and if you did you can always just minimise the other bags. The game will only put them in specialised bags if you’ve put those bags at the top of your inventory, which is your own problem.
I do put them at the bottom and they fill up with junk after my regular bags are full. It’s worse with invisible bags because I don’t even notice that junk is there because they are invisible to vendors and TP.
The option I’m suggesting would allow bags to exclude everything other than what it is supposed to loot. So if I would to only use the bag type that loots equipment in all my bag slots and turned on the option, then as I kill and loot it will only pick up equipment and nothing else because those bags will show as full for all other types of items like junk and crafting. The only time it should overflow items types to another bag would be to regular ones.