First, let me state that I purchased my T-Mobile iPhone 5 through T-Mobile.
That being said, this was my AppleCare+ purchase experience:
I had already spoken to a AppleCare rep, and they told me that I actually could purchase AC+ over the phone by providing a serial number...
When my phone arrived, I didn't even open it. I called and gave them the SN that was printed on the box label... This didn't work out, they had an error they couldn't get past. After transferring me to a different section, they told me that I had to activate it on a network first. (I was being over zealous, lol)
So I turned it on.. ran through the basic steps to get it running and connected to the cell network and activated. I gave it a couple hours for that to take hold on the systems.
I called the AC reps again (at this point they had given me a case number.. I barely had to tell the new guy anything..pretty awesome really) That time it went through without a hitch. Within a few hours I had my iPhone 5 covered, with all of the welcome emails and everything.
So, yes I purchased it through T-Mobile's online store.. but I would think that as long as it is legitimately new, there shouldn't be any issues. When you do purchase through eBay, you always get some form of BoS, same with paypal.. And AppleCare+ is linked to the device SN, not to you necessarily. (At least thats how it seems to me.. I can check the coverage of my device without signing in anywhere on the Apple website)