Was playing today, saw three cop cars parked outside Donut Heaven, and realized I hadn't tried Secret Mania in ages (because I've never had it not screw up the rest of the game). But I couldn't resist. Scored about 15M, Secret Mania ended, then...the pin played perfectly for the rest of the game! Multiball worked fine, traffic lights worked fine, and I made it to two Redline Manias - everything worked great.
So there you go - Secret Mania doesn't always hose the rest of the game. Wish I'd videoed it to see what state the machine was in when I started and ended it. Would be cool to know when it's safe to try it...
(This was with the L2 ROM.)