What I would do, and note that this is not something I have any first-hand experience with, but it should work:
As themes now can (and should) provide default configuration via config.toml I would treat the theme as a project. For this use case you probably do not need /content – generate a home page only would probably be Ok. So:
Add config.toml with params, menus, media types etc. that are needed.
Run hugo from the theme folder (not the exampleSite) and commit the /resources folder.
The problem with this approach is that most themes have a exampleSite/ with a config.toml. So you have to run hugo in exampleSite/ and commit exampleSite/resources/. This is a lot of manual work to do for theme maintainer.
Do hugo look for resources in the theme resources directory?
I’ve noticed (and documented in another recent post) that you don’t need to run and commit the resources in the theme if you don’t want to, just instruct theme users to do this themselves. assets from the theme “compile” nicely into the resources folder for the site.