Most of the league settings that are available are available at league creation. There are a couple things that aren’t. The one setting that comes to mind is letting trades pass after 24 hours instead of 48.
Category-based H2H scoring is a wishlist item that I’d like to address before 2020. The other rules you’re talking about are not really aligned with Ottoneu’s purpose. 40-man rosters and the option to keep everyone are core features of Ottoneu, and thus are unlikely to become league settings in the future.
One thing I’ll say is that Ottoneu is a lot, but it is a ton of fun (as you know!) - I think you and your pals should give it a shot, especially because leagues that are comprised of people who know each other have the most fun.