That's a tough question that may only be verifiable if you check the results with REW and a UMIK.
Possible Pro: The sub's internal limiter will be aware of the correction, this means that it can better handle large dB swings. This is what I'd do though.
Possible Con: Unlikely, but the phase shift from the correction may be a bit wonky or extreme, and you may notice issues with music.
I'd actually recommend 10-12 measurement points at and above MLP for DIRAC/audyssey. I find that I run into issues with my leather couch's headrest acting like a wall, and I get really funky mid to high corrections where pink noise post-correction sounds abysmal compared to bypass mode. I think this is why audioholics recommends bypassing correction above 1000Hz at the transition frequency (room-to-speaker). Though, I still prefer correcting the speaker full range.
Main takeaway is to play around with it and learn. That's what I did. Oh, side note, you can usually verify the pink noise with something like specdroid on android or another FFT app on an iphone.
Best of luck!