This is a pretty cool idea, but I'm not clear how you calculated Skills on the Example. Did you keep the Commoner's Skills before he was assimilated? Very confusing. With Intelligence 1, we're looking at [5 x (2 - 1)] or 5 Skill Points.
Are you presenting a Commoner who conveniently had Bluff 4(4) and Disguise 4(4), then added 1 Skill Point to Disguise and +4 from the Template? Are the Skill Points get retroactively reassigned when the Commoner is assimilated?
Sorry, if this is a bit of an odd question. I'm not clear on how this sort of thing should work.