It is unlikely that a C1 would be issued when it is not the usual, logical flight pattern to get from Point A to Point B. As others have said, since the requirements are exactly the same for a C1 and a B1/B2 visa, it makes no sense from a consular officer's viewpoint. Since the starting point for either visa adjudication is the assumption that the applicant intends to go to the US and stay, they need to not only be convinced that there are strong reasons to leave the US (and, no -- onward tickets are not a strong reason), but also that a transit visa is needed for the travel itinerary. Since there are, clearly, several routes from Cali to Puerto Vallarta that do not require transiting the US, it will be difficult to justify why one is needed.
This can also appear to be an attempt to "game the system" and using a C1 appointment -- which is much quicker to get since they are usually needed/used by crew members to get to their immediate assignment -- to get into the US quickly and avoid the long wait for a B visa interview.