Mentor will tell you this is by design. Take a look at https://supportnet.mentor.com/portal?do=reference.technote&id=MG588516&lang=en&prod=C107-S123-G192-P10287
Per that link:
According to the documentation " Manufacturing Inputs and Outputs Guide “, Pads are removed on signal layers only. Pin & Via pads are not to be removed from positive or negative plane layers, hence the application (ODB++ Generator) is functioning as designed.
There are a couple of Mentor Ideas that have been submitted, please go out and vote for these
Looking at the ideas site, Jerry Suiter from Mentor wrote back in March, "Hello, We plan to improve ODB++ to support better non-functional pad removal (similar to what is supported in gerber today).Regards,Jerry Suiter". So, that is great news. Maybe Jerry can give us an update