Factory Reset just resets your phone's memory. You still have the same SD Card, the same ESN, the same ROM, the same RAM, etc.
A new phone (such as a replacement phone) will not have the same anything except in design specs.
Because when I replaced my phone I didn't get my Free Apps back. I had to redownload it. Your Free Apps history is not saved to your Gmail account. I think it is only saved on your phone somewhere. That is the only logical reason I can come up with why Factory reset would preserve it, while a new phone logged in to your Gmail account did not.