You definitely need an exported backed up copy of your v2 settings, not the .plist file the software itself uses to store its state, internal data and other settings.
All around though, going through the new settings would probably not be a bad way of familiarising yourself with what is new, in those regards (you could probably skip a lot of the largest one, the Appearance tab, unless you have something in mind you want to change). If you’re someone that appreciates getting things set up the way you want, as it sounds like, then you might as well find out what new things you can adjust!
The ~/Library/Application Support/Scrivener folder, on the other hand, you definitely want to bring over, as that will have all of your compile settings, project templates, custom scriptwriting mode setups, potentially your automatic backups, and more. While some of that still will need upgrading, there are tools for doing so where necessary (see the migration tutorial for the details on that).
If so, that was backed up so I have it… however, I’m not sure whether I can simply copy it into the v3 Library folder, and I’m thinking that might be dangerous!
Specifically though, it’s perfectly harmless to do that, so harmless in fact nothing will ever use it. 
Scrivener 2 cannot run on newer Macs at all, and v3 is never going to read from the ~/Library/Preferences/com.literatureandlatte.scrivener2.plist file, so it will just sit there, doing nothing forever.
To speak more generally though, there is little harm in copying your ~/Library/Preferences and ~/Library/Application Support folders over bulk, and maybe ~/Library/Containers too. There may be other things in the Library folder worth copying, such as spelling word lists, custom colour palettes and so on. Myself if I’m doing a big upgrade and don’t want to simply copy my user folder over fully, I keep my old Library folder around for a long time, somewhere separate like Documents. That way if I launch a program and note I’m missing some presets or something, I can go look and see where they might have been stored.
Going from 2013 to 2026 though, I’d be selective in what I copy from Library rather than doing a full copy from the old user folder. The three main settings folders I listed above are generally safe to copy because they are up to the software you use rather than the OS. The OS isn’t going to be needing to upgrade or change them.