The look from Kirk to David and David's shaking of his head isn't just a throwaway part of the script, it's pretty important. And when Chekov read the distance off to Kirk and Kirk looked over to David, Kirk was not at all concerned about David's opinion over whether they were at a safe core breach distance. The only possible content of the exchange between Kirk and David was whether they were far enough away to avoid the Genesis Wave, which is where David's expertise is and the reason Kirk gave a querying look to David.
The concern of getting far enough away was exactly about the Genesis Wave itself, because there's no other logical reason for the visual exchange between Kirk and David.
Edit to add:
As to the effectiveness of the Genesis device within a nebula, this may have been mentioned already, but I think it's reasonable to note that the use of protomatter has never directly been proven to have contributed to the instability of the Genesis planet, and it's certainly possible that the resultant instability may have been precisely because it wasn't designed to be used in a nebula, nor interact with a simultaneous warp core breach caused by it's detonation*. The circumstances of the formation of the Genesis planet were nowhere near the ideal prescribed testing conditions for Phase 3 of Genesis. The planet may have formed from the Nebula and the other matter resulting from Reliant's detonation, so it formed, but really couldn't cut it in the long run because it had crap to work with.