All systems around the ECU are completely "free" and can thus be changed at will, as long as the regulated ECU and it's output are completely original and unmodified..
Sorry for being a little thickheaded but if I am understanding you correctly, injector sizes can
be changed but the spec Magnetti Marelli ECU's mapping cannot
be reprogrammed/ modified to adjust ignition advance, spark, valve timing an/or AFRs for example?
If so, that totally sucks, but I suspected as much.
Interestingly enough, Yamaha is in a unique position to claim their two engine failures at Mugello were the result of faulty parts which, under the current rules, enable them to open up their remaining allotted engines to make the necessary "fixes" and God knows what else to potentially make their superb motors even better.
I'll be surprised if Yamaha doesn't win the championship this year unless Honda is able to somehow make their bikes accelerate a little better than garden slugs and Marquez returns to riding over his head without the repeating the string of disasterous consequences of last year. In 2013 and 2014, he routinely rode the bike on the edge without falling down during actual races for the most part. Last year's bike, OTOH, was such a POS, he had to take a win or bin approach with a machine that simply couldn't keep up at the majority of tracks.
Its still going to be an exciting year.