That's a technical detail which probably one of the core developers might have a better answer (I don't use a Mac and am not aware of how Apple Silicon Builds generally work).

As to dumping 3.3 and solely relying on 3.8 (not 3.9), I don't think the developers think it worthwhile to dump an entire package ecosystem built in the last 10 years just for a native build.

Just upgrading to 3.8 would drop support for a fair number of plugins - python is only somewhat source backwards compatible and not at all binary backwards compatible. As for why 3.3 is difficult to compile for macOS ARM, the 3.8 port is actually a fairly large changeset that would need to be back-ported and tested for 3.3.

Are the plugins loaded in to the main ST process (using an embedded interpreter)?

A subprocess plugin architecture that used IPC to talk to the text editor would solve the problem, since the plugin host process could probably remain x86 and run under Rosetta.