That looks like a pretty good checklist to me. The keyboard settings are saved into the settings file, so that would be a little redundant—but it certainly does not hurt to have them backed up separate.
Am I correct that these backups are ideally just insurance, and that the installation should leave the above settings untouched? Are toolbars part of the .prefs file?
Yes, the installation script will in this case transition you to a new wordlist file (the encoding changed from ASCII to Unicode) and a new registry master folder, all in the background.
Toolbar is in the registry, as are any favourite projects you have pinned (which is super annoying). Do note this issue with toolbars on upgrade. Activation is also in the registry, you won’t lose that even if you uninstall.
You could of course dump the Scrivener3 registry folder to a .reg file, which could later be restored in regedit if you needed to revert. For most people that’s a bit overkill, but if you have no allergies to regedit, it’s the most thorough.
Odd, when I check for updates in my current 3.1.1.0 installation, it tells me I am up to date. Any reason why that would be?
We’re working on a fix for that. Older versions ignore anything but a .0 on the end, thinking they are beta versions. It’s a hold-over from the public beta days. You might as well upgrade via the installer though anyway, as at this point you’d have to update twice, once to switch to a version that can read the new updater format, and then to 3.1.5. We overhauled the updater code to avoid problems like this, among many other things, like an opt-in beta stream you can turn on in the software with a checkbox.