Maybe, if the Dish DVR did the formatting itself, but I think that is unlikely... but I don't know.
I suspect it's not actually the format of the flash drive (filesystem), but the format of the video files themselves, that is the problem.
The Dish DVR DOES reformat the flash drive before copying.
The issue as stated by the OP is that Windows won’t read the USB, not that it won’t read the files. It is a file system issue.
Possibly. I have worked with DVRs for video surveillance that store videos in MP4 but use some special compression algorithms so that you cannot actually view them as regular mp4’s. They require a proprietary viewer software to read the file. It’s possible that regular tv DVRs might be doing something similar.