Well, the case sensitivity works the other way. Windows names a file x, and the calibre database asked it to create X -- works fine when windows tells calibre the file is there, but linux doesn't and can't find the requested file.
And the file length is already properly worked around on Windows, but longer filenames are allowed on linux. I don't know why, but it seems to be deliberate? Possibly because there is no need to restrict linux users from having more meaningful filenames when they aren't expected to be switching to Windows all the time.
Which isn't to say there cannot be a solution -- but I don't know how worth it it is for Kovid to spend time on something that can be almost guaranteed to be used by maybe like one person.
I would suggest that at least for the moment, Remote Desktopping would seem to be the easiest solution.