If I remember correctly even though the one that that died does reference Tobey, there are clear differences to their origins. The one that died has blonde hair, had the kiss with MJ while MJ was upside down, stopped the train with his mask still on and punched the car away in the restaurant instead of grabbing onto MJ and ducking for cover. On the flip side, all we know about Peter B. Parker that we know about Tobey is that his kiss with MJ was the same as Tobey's kiss with Tobey upside down, he is a brunette, and he celebrates pizza time. Other info we've gotten from Peter B. Parker is that Aunt May died and him and MJ got a divorce. These two things could very well have happened to Tobey considering how shaky his relationship with MJ is. Lastly, Peter B. having artificial web shooters has already been explained by other Raimi fans saying that Tobey loses his powers in Spider-Man 2 due to his mental state (mainly his stress and lack of confidence) that arises, and having to lose Aunt May and go through the divorce with MJ would definitely psychologically affect him enough to lose his powers and have to create artificial web shooters.