I rank Watson higher now because for fantasy football the rushing stats help out tremendously - but I do share your concerns, especially since he's slight of build.
Agreed - "if healthy" his fantasy assets are tremendous. The rushing ability and the weapons he should have will make him a valuable fantasy asset.
That said, JimmyG arguably did more with less talent around him, and while I think the Niners will be improving on offense, the Texans should stay about the same? Maybe they bring in an impact TE, but more likely they draft one - and rookie TE's don't always have the most success offensively.
I have other concerns about the Texans QB besides his slight of build/injury risk - the Texans bread & butter is defense. One might argue that much of Watson's value was because 1/2 the Texans D was hurt this year. They had very little pass rush, they couldn't stop the run, their top defensive players were hurt or out much of the season - and all of the time Watson played.
So one might also argue that with Houston returning to health, the Texans may want to run the ball more, and have Watson manage the game more than carry the offense on his arm/legs. I'm not saying he'll turn into a pumpkin, but I have a very difficult time envisioning a scenario where Watson has to throw 50 yard bombs just to keep HOU in the game while constantly playing from behind. Unless HOU's defense tanks again, which seems unlikely.
By comparison, Garapolo's Niners played better on defense with him in as starter. He put up multiple 300+ yard passing games, and multiple multi-TD games. And with the Niners likely to spend some cap space & draft picks on offensive talent, it seems more likely that Garapolo's ceiling will be higher next season, while Watson's ceiling (and maybe even his floor) could be lower than it was this year.
Just an observation - I could be wrong here, but they played in two dramatically different sets of circumstances. And since we're discussing sample size, I have a hard time shaking the fact that Watson was beaten out as starting QB in camp by a pretty untalented QB, and only got his chance after both Yates & Heinike got hurt. So what did the Texans see in camp that resulted in Watson being behind those two scrubs on the depth chart? Obviously Watson went out and balled - but I think it's a legitimate question, and one that could be answered with more time on the field. I didn't see enough to guess at this so maybe some Texans fans here can enlighten me: was it just inept coaching that kept him down, or will more play expose flaws in Watson's game?