i can speak a bit to what parameters COBB was changing, at least on the 1gen Mazdaspeed3, not that its a huge secret. what i'm sure is assumed is that they went and cranked up the boost map and that was it, but that was not so. they found that there are several different tables that required adjusting in order to effect change. while the easy stuff like boost is a couple tables, the actual boost target table which affects the actual output of some of the other tables like wastegate duty cycle, then boost compensation A/B 1-2 gear, boost comp 3rd gear, boost comp 4th gear, boost comp 5-6th gear, max_boost, boost comp for barometric pressure, boost comp for RPM A/B, and then of course the boost limits where the ecu starts to close down the throttle and/or cut off fuel if it sees boost over limit for more than 2 seconds.
then of course you need to adjust the two sets of wastegate duty cycle tables in order to actually get the ecu to open the wastegate and command the boost level you want, but that can also be commanded higher than the table is set if there is a boost target set elsewhere that is not being met, in which case it will increase WG duty cycle to get the boost/load it is commanded in other tables. then tables to compensate WG duty cycle based on rpm and outside temp
then there are throttle curves for each gear, and on and on and on.
actually, here's a list of all the tables from the COBB website for their accessTUNER race software, there are a ton: http://www.cobbtuning.com/info/?ID=4641
so yes, if you 'hack' into the ecu and just change the boost target table, it will increase your boost for a bit, except its not set up in the wastegate tables yet to command more boost, so you won't get the extra boost right away until the ecu recognizes that, then you start hitting fuel cut boost limit, and it tones down the change you just made. all of the different tables interweave so its not as simple as it once was, but is still possible to get there.
RE: the "uncrackable" ecu - remember that a few short years ago the Nissan GTR ecu was considered "uncrackable" but COBB managed to do that and bring the first aftermarket tuning solution to market for that car. here's the list of tables for that car, far less complicated than the MS3 actually http://www.cobbtuning.com/info/?ID=4633