Remathilis
Legend
So, no. While ref's exercise judgement, they are still absolutely bound by the rules of the game. They don't get to rewrite the rules. Ever. And ref's that go beyond simple judgements usually aren't ref's for very long.
I GET IT NOW. The DM in your worldview is just another player who has the responsibility of running monsters and NPCs. He doesn't have any authority to change the rules (house rule), or setting (beyond what's agreed on by the other players; IE lets use the Forgotten Realms). So you want maximum flexibility because you believe you have the same amount of authority in deciding the rules and setting as the DM (though being limited to a single character).
Ergo, the rules should allow (feasibly) any module to be available (be it mixing of casting types, simple/complex combat resolution, etc) to interact with each other without incident (A Vancian wizard and a mana-point wizard are fairly evenly balanced against one another, as would be someone using specialties and someone who ignores them), since the DM has no right to enforce a certain ruleset on your PC ("My campaign is OS: only vancian and no skills/feats").
This creates a horrible conundrum for the players when the game assumes a certain set of rules as default (such as "roll 4d6, drop the lowest") and then shunts others to the DMG as options (such as "point buy 28 points"). If you are the type who hates rolled PCs (you have bad die luck) and would rather the certainty of 28 points, then you are put in the position of having to "ask" the DM to use the alternate system in the DMG and the DM could say no, therefore exuding more power over you in the game. However, if all the systems are in the beginning of the PHB (ala 4e or SAGA) then all are equally valid and the DM can't tell you to use one over another for your PC.
amirite?