Factorio Forums

This sounds to me like a case of "If you build it, they will come." Build the third-party mod manager you want to see, and (as long as it works on Windows) I promise I'll try it out. I might even make some pull requests.

Personally, I'd award bonus points to any mod manager that can correctly handle crop-cache.dat and data-cache.dat, but that's hardly required. Your use case may not be well suited to handling those files anyway.