Quoted from Apinjunkie:
the extra ball frequency setting is it at the most liberal, and specials are set for extra balls as well. However you don't get the extraball lit for multiplier bonus option until your multiplier reaches what would be 8x.(gotta work for that one). Extra balls can be earned at 1200000,3500000,500000 and 7500000.keep flippen!
Yeah that'll definitely make a difference.
Personally, I don't like the idea of rewarding an Extra Ball for a score milestone; that just further skews the high scores even further in favor of more advanced players. Since a Replay has no value in Free Play settings, your reward for a score milestone is the rush of hearing that sweet, sweet knocker and knowing you're having an awesome game!
For the Special, I have my home games set to award Points (when they can be). Think about it ... you definitely completed some specific action/sequence to earn that Special so you SHOULD get rewarded. But again, a Replay has no value in Free Play. Since there's generally a separate way to earn an extra ball, then the most logical prize in this scenario is Points.
Anyway, those are just my preferences. You do you -- go find out what happens if you roll it!