Caused by vanilla hopper methods only respecting vanilla chests explicitly.
Needs a full compatibility layer to function correctly.
Lithium compat must also be checked against this.

As an update, this is still being worked on. Hoppers work as expected when Lithium is not present, although the Lithium compatibility is being reworked. CaffeineMC/lithium-fabric#444

To note - this issue is partially fixed. Hoppers properly extract from even double chests now. Only in a Lithium context is there still some weirdness to my custom containers.

I am going to mark this as fixed for now, as using Lithium 0.11.2 for 1.20.1 this seems to no longer be the case