With the Online Store 2.0 stuff, are you guys using the whole git subtree method mentioned in the shopify/git docs (https://shopify.dev/themes/best-practices/version-control) ? I've been putting src/ folder in my theme and it's working fine, but they don't mention that as a viable option in the docs.
I've just tested this approach and it does work. I think the reason they don't list it as a viable option is because you can't plug a Github action directly to the main repo, and you have to keep the contents of the assets folder under version control for them to be deployed. For the former that means you need to run your build commands locally. As for the latter, having assets part of the repo would be a requirement anyway, so it appears to be a viable workflow to me too.