there are 2 spark tables for the PCM. high octane, low octane. (by "felxi fuel" i assume you mean E85 and thats a different system again.)
which spark table the PCM references is determined by the knock sensors. your high-octane table is referenced primarily until a certain amount knock events are recorded, then the ecu assumes youve put **** fuel in it, then it will flick over to the low-octane table and run on that for a while. i not entirely sure how it it resets back to the high octane, but the PCM is always hunting and testing for peak power, so i assume it wont take it long to get back into high octane. possibly key off/key on, dunno, need to read more into it.
so along with the high and low octane tables, the PCM also references your O2 sensors and has two additional multipliers "short term fuel trims" which is temporary adjustment in fuel mixture [read: lengthening or reducing the amount of opening rate of the fuel injector] then "long term fuel trims" which are quasi-permanant changes to your base VE fuel tables.
so what happens is, one of your spark plugs isnt firing well, so the O2 sensor picks up on this because it gets an occasional pulse of "rich" and it tells the PCM, "dude, something is up on my bank, im getting weird rich spikes" to the PCM says "no worries bruv, ima send you some trim to sort that **** right out" so the PCM cuts a fraction of a mulisecond off the opening rate of that injector bank, which helps bring the AFR (air fuel ratio) back into spec. everyone is happy and the car carries on.
nothing further happens, so the car is stopped and the PCM forgets that the event ever happened.
the next day that same O2 sensor says "dude, same things happened again" PCM is like "no stress, ill cut it again" and does it again. fixes the problem, everyone is happy.
on the FIFTH time, O2 is like "dude, seriously... shits ####ed, sort it out perma-style" so what the PCM does now is says "RIGHT YOU MISBEHAVING INJECTORS!!! ive had enough, im not giving you any more fuel and thats FINAL" so the PCM adds a long term fuel trim to its history and forever that bank will have gotten some fuel cut off it (at least until you either disconnect the battery or clear the LTFT history)
so thats what the tech means by "the ecu is self calibrating" in that it learns the most optimal performance for your engine given the preset parameters in the PCM.
now thats not to say you cant get your PCM TUUUUUNED.
to get your PCM tuned means youre changing the preset parameters. youre adding spark advance to high octane table, maybe telling your PCM to ignore some knock sensor events and adding and reducing fuel from your primary VE table. to get this done will cost you around a grand.
i hope thats helped.