Hypersmurf
Moderatarrrrh...
There are many ways in which a modifier can be applied and some situations where only the bonus, or possibly the penalty, will apply. In the former, they use the term modifier, but in the latter they use the sub-term (if you will). I take the glossary application, and that on page 120, as examples where only the one sub-term applies and the citing on page 8 to require both sub-terms (or "modifier" in this case). I think they were writing explicitly in all three instances, and by that logic there is no contradiction.
p120 doesn't state that one sub-term applies. It states that one sub-term does not apply : the bonus does not apply "when the character is flat-footed".
p8 states the condition under which the modifier does apply.
In the absence of that condition - "the character can react to the attack" - the modifier does not apply.
So if a character is flat-footed and cannot react to the attack, neither the sub-term (bonus) nor the modifier applies.
What is missing is an explicit definition of when a character "cannot react to an attack".
-Hyp.