Coming from Inventory Tweaks the behavior of the scroll wheel is a bit unintuitive to me. When scrolling down Inventory Tweaks used to move items from the other inventory into the player inventory and scrolling up the other way around. That way the direction of scrolling is always coherent with the direction the items move in (because of the way the inventories are usually arranged with the other inventory on top and the player inventory on the bottom). Inventory Sorter on the other hand moves items from or to the inventory slot the scroll wheel is used in, so based on which inventory the cursor is in. Obviously both ways are valid, but I would like to have the option to chose, and I assume a lot of people, who are used to the way Inventory Tweaks used to work, feel the same way.

Sadly, this doesn't work

You can flip the behavior of the wheels in the controls. Since scroll wheel doesn't seem to work in the controls menu, you'll have to set this in .minecraft/options.txt (the lines are already there, just change the numbers).

key_key.inventorysorter.itemin:-201
key_key.inventorysorter.itemout:-200

Hmmm. This should work.

I was testing in skyfactory (4 i think), mc version 1.12.2, so it could have been outdated

I don't know whether or not changing the controls in the settings works properly, but that wouldn't fix the issue I originally had with the scroll wheel behaviour. My issue was that when you scroll over items in the lower player inventory the items move in the opposite direction as the scroll, but when you scroll over items in the upper (e.g. chest) inventory the items move in the same direction as the scroll, at least if you're thinking about the items as moving up or down and not about the stack you're hovering over as increasing and decreasing. Thus it would be more intuitive to have the items always move from lower to upper inventory when scrolling up and always from upper to lower when scrolling down, and not move upwards when scrolling up in the upper or down in the lower inventory and vice versa. Simply swapping scrolling up and down doesn't fix this. Again, the current implementation is just as valid, it's just that InventoryTweaks used to do it the way I described, which is what I'm used to.