I think the issue is if Conor can't knock Khabib out immediately and gets taken down he will probably fatigue at a fast rate while beneath Khabib. His punching power/efficacy could diminish fairly quickly.
Yes, my biggest concern is that Khabib's giant skull will be able to withstand Conor's power (which is a little overblown, IMO). My general thinking on this one is that takedown defense is relatively easy to learn given the necessary athletic prerequisites. Striking is probably the most difficult element of MMA to pick up later in one's career and the hardest to be comfortable doing against the elite. I think Conor has the athletic abilities (both muscular and neurological) and the attention to technical detail to have developed very good takedown defense by this point. His length, distance management, angles, threat of striking, pressure etc. help him as well.
Khabib, on the other hand, seems to have the athleticism of one who has wrestled his whole life, which assists him in crushing his opponents on the mat. The downside to this specialization is that, on the feet, he is very stiff and slow for an elite LW. I am confident he will lose within his next several fights, even if it's not next Saturday.
The best paths for Khabib are: (1) Homer Simpsoning Conor, or (2) getting early takedowns and draining Conor's energy from him in a snowball effect