I do not know why companions have one less in each attribute in stats, my best guess is that all NPCs get +1 in each attribute as a compensation for gear players might collect during the course of the game. Companions are normal NPCs until you hire them, so if my speculations are true, they need to have stats in Character.txt 1 lower than the final desired stats to achieve the results we see when we hire them. All enemies need to be adjusted accordingly then too, but it is not more than speculation from my side, no confirmed info.
Didn't read the whole text (so maybe I don't get the problem right) but as I wrote in my guide: the difference between the nominal value in Character.txt for companions and the ingame value when you hire them comes from the act part (3). Attributes defined in Character.txt get increased by a certain formula depending on the 'level' (act part). http://larian.com/forums/ubbthreads.php?ubb=showflat&Number=582571#Post582571
I couldn't figure out the exact formula (s. my last post in the guide thread), but I gave an orientation.