Gentoo will allow you to update the small set of required system packages and their dependencies separately from everything else (emerge --update system), but doing the reverse would require some pretty heavy micro-management.

There are a lot of command-line tools for text, like grep and sed, that don’t work on binary files. Whether this matters to you depends on your workflow. (I use grep a lot.)

exFAT is a Microsoft creation that (unsurprisingly) doesn’t understand or preserve Linux-style file permissions. Neither did any of the FAT varieties before it. So the permissions on the files when you get them back relate to the mount options you pass to the exFAT drive (in this case, you probably want to set dmask and fmask), or the permissions on the directory it’s mounted to.

If you don’t want to twiddle with mount options, you could reformat the external disks using Linux-native filesystems like ext4, but you’ll lose the ability to mount them on Windows if you do that.

Windows just worked.

Excuse me while I laugh hysterically while remembering the sorts of Windows issues I’ve troubleshot for family or coworkers. The one where the combination of a particular Windows version + a particular MS Office version + document previews being activated would cause Office to crash randomly on operations that had nothing to do with document previews was particularly memorable and difficult to figure out. The various Linux snafus I’ve had to deal with were pretty easy to handle by comparison.