There's maybe a handful where I'm not sure, if you can do them via settings.
One where it's technically the case, is that they remove Pocket at compile time. But to my knowledge, Pocket integration is pretty much a glorified bookmark. There's not much code to remove. And it can be disabled via about:config by setting extensions.pocket.enabled to false.

I guess, to be fair to LibreWolf, Mozilla has been helping out the Tor Browser devs since forever, so most things needed for Tor Browser are just a toggle in the Firefox settings.
As a result, though, there's also lots of settings, which partially need expert knowledge. So, there is definitely room for different presets. But yeah, still leaves the question, whether one really needs a different executable to adjust these settings.