Now onto golf and other sports:
The average player playing on a US Open golf course from the US Open tee's would face the same challenge as a beer league softball player facing off against Randy Johnson pitching from 40 feet away. Doesn't matter if he's holding a brand new Louisville Slugger or the highest tech composite bat, he can't win that matchup.
At every level of baseball, there are equipment specifications on both the ball and the bat. While baseball may "share" the balls, in a "shared equipment" game such as football they do not. Each team provides their own balls for both their kickers and quarterbacks, as long as those balls meet the specs of the game their fair to play, which is the same we have in golf. In the NFL that ball must come from the same source, but for College, High School, and below that is not the case. Also, at each level, the specifications on the ball are different.
Brandon Finnegan would argue against your final baseball point. In 2014 he played in both the College World Series and MLB World Series. With how the draft is structured in baseball, the age ranges in baseball are extreme. Als, players hop around leagues and regulations all of the time. you get called up from the minors to the majors, different ball. You play on a High School team and a travel team, a different ball. In college, you play for the SEC and then play in a Cape Cod summer league, a different ball and a different bat!
The game is already bifurcated and gets further and further bifurcated every year. We allow it to get further separated by not building in steps to curtail the gab. Nearly every sport is bifurcated across all levels of play, but for the most part, no one really cares. Why should golf act holier than thou?
Finally:
The initial velocity regulation has been in existence for a long time. While the background behind the regulation may need some updating, All Mark did was to adjust his club back to how they were set up 25 years ago, when that ball was commonplace. The results are not surprising. He of course was also aided by the performance advantages in the design of the head that didn't previously exist.