Supposedly TDA is planning to clear futures transactions in the future. I say supposedly because they haven't given any timeline as to when that will happen, so who knows...
I emailed them last week to check and see if Penson or TDA was holding the funds for futures accounts. The response was:
Thank you for the email. All equity funds are held by TDA. Funds for Futures accounts are currently being held by Penson until the Futures transition to TD Ameritrade takes place.