I suggest you search the forums more. I spent a good 2 weeks reading every post I could on subwoofers and the consensus is, that your subwoofer will be out of sync with your main speakers, if the calibration of the subs is done separate from the calibration of the speakers.
Do you have like one reference / link?
To clarify a bit:
That a subwoofer has DSP doesn't mean you have to use it. If you have Dirac or whatever centrally, you might as well do all calibration there (including for the subwoofer). But it doesn't matter to Dirac if the subwoofer has DSP built-in.
If you insist on doing both, you can still avoid timing issues, simply do the subwoofer calibration with the subwoofer DSP first, and then the central calibration. The central calibration process will measure the latency of the subwoofer and correct for it. The latency is also typically the same no matter if you use the subwoofer DSP or not.