Wow, Preserene---you just made my eyes cross with all that info. Let me answer what I can in pieces:
99212 vs 99213: The E&M level is wholly dependent on the key components documented - hx, exam, & MDM - in the chart note. I wouldn't presume to choose an E&M level without looking at the documentation, but based on dx of HTN, DM, & vag inf, I should hope there's enough documentation to warrant at least a level 3.
Presence of Physician: I'm assuming, from the original question, that the patient saw the physician for an exam and did not come in for a simple BP/glucose level check. The physician is the one who determines what the follow-up plan is. Again, a determination cannot be made based on the info above. Only the doctor & chart note will dictate the level of follow-up exam needed & done.
Preventive + Problem E&M: You are correct. If pt presents for routine preventive exam and a non-trivial problem is encountered during said exam, then a separate E&M code is billable. Again, E&M code will be based on documentation. Physician/NPP must document this separate and apart from the preventive documentation. "Separate and apart" are key words - best CYA bet is for physician to document as a wholly separate encounter. Modifier 25 would be used on the problem E&M code in order to separate it out from the preventive code.
Vaginal Culture: Yes the lab is going to bill/code for the actual vaginal culture. The physician would bill for evaluating & managing the problem only.
Phew--did I answer all your questions?
Becky, CPC