Methodology is terrible. You shouldn't punish playrs for being dominant, but you should punish them for not winning. Every masters that passes and a given player is active in their tennis career should lower their total score as well, not just playing in it and not doing well. That would be to prevent "one surface" type players from only having to count tournaments they primarily only played in. This unfairly punishes truly injured players and people that had overly long careers, but it's much better than punishing people because they are good and favoring players that weren't good. Heh.
How do I punish players for being dominant? The 6th best result rule is actually mant to punish players who don't dominate but play an event all the time and have a lot of 4th rounds or quarterfinals.
Sampras got maximum points for his 7 Wimbledon wins, as did Agassi for winning Key Biscane 6 times.
As for favouring one surface players, they get punished too. Results for all slams and all tms events are counted, so a player who only excells on clay (Kuerten is a good example, even though he had some hard court succes) gets surpassed by a Courier who could play on all surfaces.