That would depend on a couple of factors.

Looking at the info provided by Pioneer it looks like bi-amping the front channels with the head units is going to work, however the other channels are in question, and while the amp says 50 watts that is a stretch with a bit of marketing added in for good measure if it is a BTL amplifier design. The limit there is about 20 watts per channel and that is really the top end, so if CDT recommends an amp of a certain size you might want to see what that is for comparison, and see if their crossovers allow for bi-amping.

If your going to use the factory amp to drive the factory subs, then the factory amp needs to see a full range signal and if you configure the radio the way you are talking about doing you, will be restricted to pulling that signal from the back channels. If you don't use any of the processing in the radio then it should work, but engage anything from the EQ or the surround modes and the signal will be altered (surround information) and as such be out of sync with the front channel content (no bass and rolled off high end with its of reverb).