Seems like there is a common issue between AE2 and your mod, after searching a bit none of the closed issues solved my problem, so I tried to figure it out.

I'm playing on FTB Skies, v1.0.6 (1.19.2)
Using Inventory Sorter 1.19.2-21.0.4 and Applied Energistics 2 appliedenergistics2-forge-12.9.2.

If I disable Mouse Wheel click, I can request to craft an item.

Tried running:

/invsorter bladd ae2:wireless_crafting_terminal
/invsorter bladd ae2:craftingterm

None worked, so I checked what was the last container I sorted and the response was Last container sorted: inventorysorter:dummyplayercontainer. Always this.
Tried on a chest, hopper, barrel, anything, but it was always inventorysorter:dummyplayercontainer.

Is it possible that the mod is ignoring the blacklist?

still an issue with release 23.0.1

Looks like this issue was previously opened and closed (#140) and some fixes were committed but there was also a comment that 1.18 was not being supported.
FTB Skies which is 1.19.2 has this issue and like mouro001 stated, the blacklist is not being honored and therefore you can only have one or the other, sorting in chests with middle click or AE2 auto-crafting.

This looks to either be still an issue and was not fixed or more likely has become a problem again in the last year since the previous issue was closed?

Can confirm, blacklist is being ignored.
Minecraft 1.19.2
Forge 43.2.11
Simple Inventory Sorter 21.0.4

Running into this on ATM VocanoBlock as well. Not only is the blacklist ignored, if you've added specifically the crafting terminal, or the pattern encoding terminal via the commands, you cannot remove them again via commands, it says they are invalid strings. I had to manually edit the server.toml to remove them.

Forge - 43.2.14
inventorysorter-22.0.0

This is still a issue on 1.20