First, it's awesome that you're getting personal help from Rippetoe. Like guinness said, mention Elite next time you email/call him (and feel free to pass along the appreciation of everybody who's bought Starting Strength).
IMO, you should definitely try the routine he gave you. Its provenance pretty much guarantees that it'll be effective, and it'd be really interesting to compare the results to those others have gotten Bill Starr's single-factor.
Regarding the diet advice, the relevant thing to keep in mind is that he's a strength coach, not a bodybuilder. That statement isn't intended to imply any value judgment; obviously, there's a ton of overlap in the types of methods that are effective (of which many in the latter group are almost wholly ignorant), but, equally obviously, there's a different set of emphases. Bodybuilding has, in essence, the aim of maximizing muscle mass and minimizing bodyfat. For strength training, it's gaining as much functional strength as possible for athletics. The combination of diet and training that guys like Rip advocate will maximize this variable; conditioning drills and practice before and during the sports season then naturally takes care of a lot of the fat gained. You're quite right that you'll gain more fat with the diet he gave you than with a mildly hypercaloric clean diet. Ultimately, it's just a personal decision based on your short- and long-term strength and aesthetic goals.