More research would certainly shed some light on the matter, but I doubt anyone will be rushing to conduct such research. There doesn't appear to be a clinical need for such a practice (i.e. our children born by CS aren't for some unknown reason, immunocompromised or sicker than those born vaginally), and there are risks involved that may halt progress through a research ethics committee.

There is also the practical consideration that most neonates are "towelled-off" once they are delivered - we rub them with towels to a) stimulate the baby and b) remove vernix and other secretions that might make them too cold before wrapping them up. In this process you'd certainly remove anything you put on the baby off a swab, and short of sticking it in a baby's mouth or on other mucous membranes there isn't going to be much of an inoculation (and I certainly wouldn't be comfortable doing either!).

I apologise if I was unclear - we don't swab and treat during vaginal delivery. At roughly 36 weeks of pregnancy, the patient gets tested for GBS (group B streptococcus), a normal bacteria present in the vagina in a percentage of women but that can cause serious infections in neonates. If a woman tests positive for GBS, she is given antibiotics when she goes into labour and every four hours thereafter until she delivers - this is standard practice in Australian hospitals.

Typically the patient receives a broad-spectrum antibiotics (i.e. they work on a wide range of bacteria) such as penicillin G or cefazolin to ensure the baby doesn't become colonised with GBS.

All antibiotics can cause changes in vaginal and intestinal flora, but given the relatively short duration of the course I doubt that there is any clinical significance to this. In a risk vs benefit analysis, it is far more important to ensure the baby is protected from GBS than to ensure vaginal/intestinal flora remains 100% the same as before delivery.