Fair enough. Obviously it’s going to depend on the capability of the in-car software.
I don’t have anything classical on my flash drive (which is synched with the server on an ad hoc basis from time to time) so I haven’t personally seen that problem.
I think you are right that, even on my car, when doing sort-by-title, it does not show the album name until it starts playing. However that specific kind of duplicate (same title but not actually the same track) seems rare enough that it hasn’t disturbed me.
(Digressing further, on my internal web DLNA interface to the audio collection, I have specifically set it up so that it clearly distinguishes in the title between the above type of duplicate and the other type of duplicate: same title because it is actually the same track and just happens to occur on more than one album. This is achieved by altering the title on the fly when doing sort-by-title - and even then may be somewhat heuristic but it works well enough.
So I guess in theory you could do that as the music is copied to the flash drive. That would mean that you couldn’t just copy to the flash drive using a single command and would instead need a shell script or program. Alternatively, you could fix it up on the flash drive retrospectively.
If doing in a shell script, and assuming MP3, it looks like you will need to use the id3v2 command, or similar, to mess around with the MP3 metadata in the copy on the flash drive.
Worth a shot?)
FWIW, my car seems to remember correctly exactly where I was up to - and simply continues on - even after the flash drive has been removed for a while.
Perhaps next time your car is in for service, you should see whether a firmware update is available.