It sounds like what you want/need is something like a 5MiLB system that a number of leagues use (5MiLB system for already existing league - #8 by runfolk has some info, but if you search this community for 5MiLB you’ll find more). Some leagues also do 10 or 15 MiLB. A word of warning: doing 5MiLB (or 10 or 15 or whatever) changes the economics of the league such that player values are not the same as other leagues. It also makes your league ineligible for the Ottoneu Prestige League, if that is something you are interested in. One of my leagues uses 5MiLB and it’s fine, but I definitely prefer leagues without. All up to your taste.
As for the flex on roster spots (fewer or no 5th OF or whatever), Ottoneu was pretty specifically designed to mimic MLB roster building, and MLB rosters typically carry 5 OF and at least 5 RP (I would argue they carry 5 actual RP and then 2-3 guys they are willing to throw out in mop-up duty or a game that isn’t as important) plus a bunch of others on the 40-man roster as depth/future value. That’s not an area I would expect to see customization.