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you are getting it,
things like nistune and hondata use the solder in boards usually attached to something like a "debugging port" used for development by the OEM's i assume, and that is how you gain access to the data channels and command the ECU to read from an external (daughter board) eeprom location, or while live tuning there is ram allocated for the timing/fuel tables etc that you may be editing, when you burn the file at the end of the session you are saving the changes to the daughter board's eeprom so that it can be read directly after you disconnect the laptop.
The firmware varies in complexity, some "suites" use all factory protocols, others eliminate things like EGR function and others still completely re-visit the logic that controls the engine...
the huge change came when the ECU's were required to be upgradeable via obd2 port, now it is really just a software issue, it doesn't have to be mysterious, you can be as clever as to plug the dealer tool in and re-flash while watching the com lines and seeing what packets are being sent and received to get a rough idea of the protocol required to open the flash port.
I'll have to try and remember to look again but i had seen somewhere that the Denso ECU is using a very similar address file to the diesel H4's in other subaru's but with some of the original spark and fuel tables used in their historical gas injection motors....I also believe the ECU has already been dumped for analysis (by other than ECUtek)
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