Caching/minifying plugins can be a pain for sure.
Do any of those plugins allow you to manually specific which files to minify/combine?
I know in W3 Total Cache if you choose “Combine only”, it works great with GeneratePress.
This post is also super useful for caching/minifying plugins: https://generatepress.com/forums/topic/google-speed-test/#post-122818
Let me know 🙂