MacBook Pro (Retina, Mid 2012) can support an HDMI-compatible device on its HDMI port while also using two Thunderbolt displays.
http://support.apple.com/kb/HT5219#dispnum
Seems like this question has come up a lot on here and now we have an answer.
The other FAQs also have interesting information about using different combinations of Thunderbolt displays, iMacs, and Mini-Displayport displays/adapters.