Would it be better to reformat the D and E drives as exFAT if I can cycle the content through another drive or something? I'd like to be able to access those two drives under both Bazzite and Windows.
Ideally yes.
If you can't then it will still all work most of the time but occasionally the drives will unmount from linux with block errors etc and will not work until you boot windows and run chkdsk. You can use ntfsfix on linux but it doesn't always work.
