Imo it was the right call. Linux filesystems, file attributes are different from Windows, and the two never would've been completely compatible. The two big ones, are the execute bit, and the very fact that windows files represent the data on disk, while Linux ones are just a hardlink to the inode.
It is what it is. My workflow is that I rsync the relevant files from Windows to Linux, do the work, and rsync them back. It's clunky but works well enough.