If we are going to modify our development pipeline to remove wds from the picture, then we should make that decision carefully and clean up after ourselves.

Are we sure? Granted, the build pipeline differences have been problematic. WDS does however make claims about its superior speed, we might be slowing things down dramatically by switching to Rollup. But maybe that is fine in the interests of "get it working" and we can revisit WDS later if we start getting reports about slow build speed?
Something else to check: removing WDS means removing the ability to debug in any context other than a Tauri window, which means foregoing Firefox Devtools features and other development tooling plugins. The only way to debug elsewhere is via WDS or similar.
#7 (comment)

Thinking about it more and bypassing WDS may also mean breaking HMR which is really going to slow down development a lot; would you mind testing with your working app to see if you can successfully hot-swap a component? If that's not working then I think we should put some time into getting WDS working again and run hc launch pointed at a URL rather than a file so that a HMR-capable dev env can run through it.
#7 (comment)