If your issue is that cover images are not being written to FLAC files, then when you reload those same FLAC files into Mp3 tag, their covers should be missing. Are they in fact missing? If not, that means the covers are being written to your FLAC files by Mp3tag but Explorer is simply not showing them. That is a whole different kettle of fish, as they say.
Your MP3 vs FLAC icon display issue may reflect a difference in your Explorer View settings for the parent folders for each type. Try using larger icons for FLAC.
If that fails, there is an excellent freeware utility called Icaros Shell Extensions that will almost always solve icon display problems in Explorer (which are very common). I have used it for many years.