I never did try a 27C64 but I'd assume there'd be no issue until you tried to save data to it. It may just fail quietly or it may stop the game in it's tracks. Hopefully it'll keep playing and only changes data when you do so in settings. If MAME can run this game at some point then in theory you could set up how you want your cab set up in MAME then take the timekeeper file and burn that to a rom.
To program the M48T58Y with a normal programmer you need to short pin 26 to pin 28 as pin 26 needs to be held high when programmed and read. If you get an error right at the end of verify don't worry. It's a time keeper and the last couple of bytes are the current time
If you programmer directly supports it you should be ok though.
These ICs will all be dead at some point and I'm pretty sure they have not been made for a long while. If you bought some NOS I'd say they are well into their shelf life.