In order not to look for answers, you can install those chips yourself that you consider necessary
Nice replay
I will definitely do that in near future.
on topic now
As for MT41K256M16TW-093 that was what I found available on stock, seems compatible but I'm not 100% sure, from datasheet looks like some data lines are splitted in lower and upper.
Just for example on video cards when replace RAM chips there are some some config resistor that you need to change based on chip vendor, it may be different pinout but I don't think so.
So best approach will be to use same chips as original ones.
I don't think they are separated, data lines are shared, to check for some activity on this chips you must be doing this only on specific pins that are used only by that memory chip under test, chip select or chip enable (maybe some others too) and if there is firmware on that 25Q128 and is different from models with different RAM size then you also got nothing since FPGA will not try to use them so no activity an dedicated pins.And now we can't be sure for anything.
Some say that 25Q128 is used to store some initialization for FPGA and firmware is loaded by startup script, a little strange to use 16MB chip only for that, if my memory serve well that firmware or boot from FPGA folder is around 4MB