After second round they still aren't vaccinated for Rabies yet (unless you're in Florida, sometimes they do it at 13 weeks I believe). So, while it's probably unlikely a bat will swoop down and bite your chi, it's better to be safe than sorry! =) Good point about the DHPP vaccinations too, although they are "boostered", it isn't until the third booster that you can be sure they are immunized (~20% dogs immunized by 8 weeks, ~60% by 12 weeks, ~90+ by 16 weeks). Each dog's immune system works differently, which is why they are boostered at each stage to ensure the vaccine has greatest potential to build enough antibodies.
Although it might seem ironic, the most critical time to shield your puppy from other people/environment, is at the animal hospital. Here is the highest concentration of diseases and communicable illnesses, and it's also the place your puppy gets vaccinated. So feel free to bring your pup in a carrier, let people know it's not vaccinated fully if they want to touch, keep it away from other dogs, and feel free to put your own blanket down on the exam table. =)