I think it would be pretty easy to ferret out cheaters in an online leaderboard, especially if the rest of the pin is integrated.
It's not that hard to determine "impossible" switch sequences, or even switch sequences that just don't make logical sense, like all of the targets for a certain mode being hit, in order, without the flippers being hit (as a very elementary example).
As an even simpler deterrent and additional feature set, you could always add a webcam covering the playfield. Your "scoring" game is recorded and uploaded along side your score. Want to see how someone got that high score? Watch the replay of their game and see what tricks they use. Want to remember the light show that happened when you hit wizard mode? Just archive the replay so you can see it whenever you want.
What about making the platform open, so people could build toolsets and catalog knowledge around one strong platform, and even use it to their benefit in older games through emulation.