1. Does it have current code? Never seen that before

This is normal for WPC games. You can fix or replace the flipper boards as usual to get rid of the credit dot, or just live with it.

1. the flipper switches or the flipper eos?
2. take the phone off via the two lock nuts, then remove the mounting plate, then get your fingers in there

This. WHICH flipper switches?

My first guess would be that the flipper button optos for the upper switches are bad, might have gotten swapped with lower in the past as they're not used. Not something to worry about either way.

Yup!
Or they're stuck closed because of dirt, heat, dust, whatever. You can go into Switch Test and press the flipper buttons to see what they do, if anything.
In either case, it won't affect your game, other than the credit dot.

2. take the phone off via the two lock nuts, then remove the mounting plate, then get your fingers in there

Yeah it's funny this question came up since I just replaced the flasher in my phone yesterday. The lock nut at the base of the phone in front needs to be removed, and the one behind the phone only needs to be loosened because then the plate will slide out because it is slotted. That is good because it would be impossible to get that nut started again with the phone in place with no room to fit your fingers behind it.

ah, good to know. I replaced mine while doing a full teardown so I had easy access to both nuts