If autoCraftingTable is set to true a crafting table pressed into a hopper minecart will not drop its items into a hopper below.
setting autoCraftingTable to false the hopper minecart will drop its items.

carpet mod version 1.4.23
carpet extra mod version 1.4.23
autocraftingtable mod version 1.4.17
minecraft 1.16.5

Sounds like vanilla functionality. Doesn't the same happen if you replace the crafting table with a chest or another container?

IIRC Minecraft disables hoppers polling for entities when they have a block entity above, therefore the hopper minecart entity is ignored.

(with autoCraftingTable, the crafting table becomes a block entity, since it has to store its inventory etc)

Yeah, that's a standard behaviour of a hopper - if there is a container above it / in it - its item pickup behaviour is different.
That's a trade-off for enabling container properties for a block conditionally - that happens with the crafting table extension (one of many reasons its not part of any standard carpet pieces) - you get inconsistent behaviour. If crafting-crafting table was implemented as its own separate block (properly modded, not 'pretend-vanilla') than everything would be all good.

For more consistent approach, I suggest you use craftingDropper from extra