Yes, test the normal mapping apart from the HIROM:ALL stuff! Basic test would be to just program the cart with the menu on 1st chip and with normal resistor setting. That should supposedly work even if the 3rd chip is installed (?)
And then change the resistor, theoretically, the cart should then still be able to read the menu from the 1st chip - if it doesn't work then there strange things happening.
Did you try the unknown Port[2400h] commands to see if they affect the mapping. And especially, did you try Port[2400h]=21h, since that command is known to disable ROM on a cart with 2 chips (and might thus activate the 3rd chip on a cart with 3 chips).
Might be best to try the above stuff with the resistor both at default & special locations (as by now, the special resistor setting didn't seem to do what it was expected to do, so maybe it's having some different purpose as expected, like activating a special mode with one large FLASH instead of 2-3 small FLASH chips, or whatever).
Are you sure that your 1610 chip outputs F1h as device ID? And what's its exact part number? The device IDs known to me are:
FAh = MX29F1610A ;\with sector_protect, suspend/resume, without sleep/abort
FBh = MX29F1610B ;/
F7h = MX29F1611 ;-with sector_protect, suspend/resume, sleep/abort
6Bh = MX29F1615 ;-without sector_protect, suspend/resume, sleep/abort
F3h = MX29F1601MC ;<-- undocumented, used in SNES nintendo power carts
If two chipselect's are triggered simultaneously, then you might get two ID's ANDed together.
On the other hand, with above values, that would never result in F1h. So yeah, I guess must have some chip that isn't in the above ID list.
I am not sure if I can follow you on the what-is-in-which-bank stuff. Having data in banks 40,50,60,70,C0,D0,E0,F0 makes sense to me - but didn't clearly say when there is no data in those banks.
Normal HiROM mapping should mirror the upper 32K-halves to those banks, or is that different in "HIROM:ALL" mode (with default resistor setting), and there's nothing mirrored to bank 00-3F and 80-BF in that case?
Btw. if you want to use the FLASH commands with port AAAAh and 5554h, did you recurse that bank 00-3F and 80-BF are only 32Kbyte in size? Ie. the FLASH commands would be then written to 01AAAAh and 0D554h. And chio ID would be read from 00800xh.
EDIT: Or as you said you get that weird interleaved mapping at A00000h and up when changing the resistor: That's apparently not following the normal 32Kbyte mapping. On the other hand, in that case, AAAAh and 5554h would need to be converted to interleaved addresses, which should be A05555h and A02AAAh (ie. divided by 2, plus A00000h). Hope that's right, the interleave effect is quite weird & confusing.
If everything doesn't help: Maybe nintendo has mis-wired the PCB (to me, FLASH_CS3 would look better at pin73 instead of pin71, but I hope that they knew what they were doing, and then pin71 should be okay).