The issue of dual applying in gen surg and CT at the same institution is an important one. By and large, expect to be rejected by the gen surg programs where you've applied for I6. Anecdotally, given my own experience and that of fellow interviewees, dual invites were offered at Duke (they have one interview day for both programs, and are by far the most accepting gen surg program of I6 candidates), Northwestern, USC, Yale, Cleveland Clinic, and University of Washington. Because the gen surg interviews you get are highly unpredictable, most of us dual applied to most programs and hoped for the best. There are duplicitous gen surg programs that offer an internal 4+3 option and yet reject all I6 candidates, and in one instance, a program director mused to me about how she's surprised that so few general surgery residents have gone into CT and availed of the 4+3 option.
Your second question surprises me. Successful I6 candidates have demonstrated extraordinary commitment to CT surgery throughout medical school and even beyond, and if you are unwilling or unable to actually explore the field via subIs and strive for letters from CT surgeons, you might be better served applying to general surgery alone with the option of a CT fellowship later. While traditional fellowships have dwindled a little due to I6, almost every program I interviewed at this winter expressed a commitment to continuing the traditional fellowship in the foreseeable future. In fact, I was surprised by how many faculty at even well-established I6 programs felt that the traditional model is the best way to train a CT surgeon and expressed open and even vehement skepticism of the I6 model.
