Those custom rules were added before edopro even existed in 2016. Just you didn’t know about them until after edopro got released in 2020. The idea is that each of these rules were lua scripts that were preloaded into the duel.
It’s taken 8 years for people to even discover that these custom rules existed all this time. In Omega, we have the duel rule option which allows you to select official duel rule formats. This is because the average user doesn’t know what rules are in what format, let alone the sheer number of different duel rules.
Even in edopro, people are still discovering this as we speak. Omega is currently 1 year old and we plan to keep expanding things but the priority is not to duplicate what already exists, but to add features that have never existed like tournaments.
Everyone wants what ygopro already has in omega and that will come with time. Features like offline AI will automatically bring puzzle mode and offline test hands. Features like all these custom rules will come in the future but it’s not a priority atm. If we added this now, it would just overcrowd the UI even more, cause more menus and options to be created. Users have yet to even learn the current options that exist in Omega.
You talk about fractions, but master duel will have even less than 1% of the customizability that ygopro or omega will ever have and that is because no matter what the customizability a game has, the mean feature of a game must be the primary game mode with official rules and official banlists.