In tournament play on TZ you remove the ONE powerball from the machine and set the machine settings to no ceramic ball/emulate powerball every two gumball machine releases. Thus for every player the 'powerball' (now a real metal pinball) is released every two gumball cycles from the gumball machine. you can tell when the machine is doing emulation or tournament powerball rules since the powerball message (shoot gumball) on the DMD will be in REVERSED colored text (orange background black text).

As far as the locked balls not being dumped, There is no setting to get it to dump them after game end, the only way is some sort of boot cycle (into diag and out, power cycle, slam tilt, etc.).

No matter what, the ceramic ball may not be in the gumball machine at the start of a game. That's just the luck of the draw where it starts at (which is why you REMOVE it for tournament play). So that everyone is on equal footing (two gumball releases for powerball shot).

Thus your description of the powerball being the only ball in the trough is a normal occurrence on a TZ, in theory, on location the powerball wouldn't be the only ball in play very long (since one would tend to shoot the powerball back into the gumball for powerball mania or into lock to save for later). Consider it a bonus to a machine you walk up on that the powerball is the only ball in play and you get off to a good start with extra points you didn't have to work hard for.