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I don't think so because the part numbers are different. ZJ80's apparently also have two different ECUs, changing in '95.
I believe that the FZJ has two ECUs because of the mid model required implementation of OBD-II (93-94 are not OBD-II). That likely had a direct impact on the hardware due to the standard OBD-II diagnostic output and port requirement. Oh and they changed from AFM to MAF at some point. That might impact ECU design (at least the data tables).
There are a couple of subtle differences for the '80 3FE. The alt is, I believe, 90 amps (at least some of them are). Overhanger at one point told me that the ignitor has more output. Not sure if there are any other emissions or other differences that might influence ECU differences.
This thread may offer some insight.