River, I believe the loop mode adjustments that can't be changed are there to ensure the unit is street legal. Even though those areas can't be adjusted they should ensure proper mixture ratios with the AIS removed which is something the stock unit doesn't do. Before purchasing one I would talk directly to the folks who make the Power Comander.
If Yamaha were to allow the stock unit to readjust for proper AFR with the AIS removed then it would never get past EPA testing. They are limited to producing a unit that passes when in the stock configuration.
I am in agreement with you on that Scott, 100%. Non of these units come with a programmable ROM that I know of, you can buy chips for cars or even burn them yourself, but I don't think you can get them from the factory. Knowing that, I don't need to talk to the the folks at Power Commander to know what they are doing, they are simply manipulating the o2's to go the the desired voltage an perhaps lengthening the hold times on the injectors. One of them claims their little computers have faster sampling times, like 80 times per second and it probably does.I don't know what good that does exactly over the sampling times of the factory computer. How many time a second to you need to sample the voltage on an o2? Ha!