Use relationship for Views taxonomy term filter
I've been able to do this with a simple "Content: Referenced product" relationship in my view. If you try using any of the "Content: xxxxx" filter fields, they won't work, as you're noting here. So, "Content: has taxonomy term ID," won't let you choose the relationship.
However, if you use the "Commerce Product: xxxx" (where xxxx is the term refrerence field) field for your contextual filter, it'll work with the relationship.