I'm not sure where it specifically says you don't get bonuses.
It doesn't specifically say you can't get bonuses anywhere because it shouldn't have to. Thaumaturgy outlines how a spell is built and can replace a skill--there is no provision for how to make a spell to give a bonus to a skill, whereas the mechanics are in place to replace it for a roll--the Contest rules. The only place where bonuses to skills w/ magic is discussed is in the potion examples, which are god-awful and shouldn't be referenced, period. If you want to get several rolls in a row replaced, then you have to add the replacement for each roll up--for instance, if you wanted three Fight replacement rolls at Great (+4) you wouldn't need just 4 power +2 shifts for more duration, you'd need 4 power x 3 rolls = 12 shifts.
I think we 'discovered' this a couple months ago, but this is the only way you can get multiple replaced skill rolls with one spell.
The non-beta book probably clarifies it.
It does not, unfortunately.
Does the armor bonus from inhuman (or otherwise) toughness stack with actual armor, or is it like the magic items?
Not per the RAW, no. Armor doesn't stack with other armor, excepting the one blunt damage stunt.