I gotta say I'm with Ray on this one. If the FAQ says it's a modification to their "base characteristic" then I think they've been as explicit as they're going to get on the matter. Hopping on a Thunderwolf alters the profile itself, making the rider always S5. There is no standard situation (special rules of enemy psychic powers or wargear or whatever notwithstanding) in which he would attack at any less than S5. He can't get off the wolf and fight separately, so the wolf's strength becomes part of "the model"'s strength.
Furious Charge is a temporary modifier (a bonus if certain in-game criteria are met, if you will) and therefore follows the normal flow of multiply then add/subtract then fixed number. A model with Furious Charge does not get the +1 S if they are charged or in the second round of close combat, so it's a very different situation.