Add support for Instantiate for BlackBox, ExtModule, and IntrinsicModule (#3349)

* Allow IntrinsicModule to be used in Instantiate

Change a few `RawModule`s to `BaseModule`s to allow for intrinsic
modules to be used with the instantiation API.

* Add tests for Instantiate of non-RawModules

---------

Co-authored-by: Fabian Schuiki <fabian@schuiki.ch>