1. The bottom position in MMA is significantly worse and more dangerous than the bottom position in a grappling match due to striking. This is not an opinion, this is a very simple and inarguable fact based on elementary physics: the person on the bottom cannot put his bodyweight into his strikes and thus loses pretty much all of his power. Anything the person on the bottom can throw, the person on top can throw much harder. If the bottom position is considered inferior in pure grappling, then it's even more inferior in MMA. Any effective striking coming from the person on the bottom is achieved by overcoming the disadvantage via superrior skill, not because there is no disadvantage.
2. Khabib did not spend most of his time in RDA's full guard, he was either trying to take RDA's back or was in half-guard. In fact, moments when Khabib was in RDA's full guard were very rare and you will have trouble naming them.
3. Khabib landed at least 6 very powerful and clearly audible blows from top in the last two minutes of round 2 alone. That's infinitely more than the damage RDA delivered on the ground, as he delivered nothing.
4. It is irrelevant what "many believe", what matters is the ruleset and the rules clearly award control time to the fighter being in top position, which means that the top position is considered superior.
5. Damage is the main criterion according to which
effective striking is scored, but effective grappling is not scored only or even mainly on damage. The rules clearly state that takedowns (those leading to established offense), achievement of advantageous positions, submission attempts and reversals are all important as well along with damage.
These are not my opinions, these are literally the rules and nowhere in the rules does it say that damage is the main criterion (or a criterion superior to others) according to which effective grappling is evaluated:
https://www.dca.ca.gov/csac/forms_pubs/publications/unified_rules_2017.pdf
6. There is also nothing subjective about Khabib dominating RDA. On the feet, both fighters were more or less evenly matched and barely landed anything. However, on the ground, Khabib was winning the grappling engagements from start to finish with the exception of RDA's guillotine attempt. That's it, that's ALL RDA managed to do on the ground throughout the entire fight. Since according to the ruleset grappling engagements can be won via multiple criteria with damage being only one of them, there is no question that Khabib dominated RDA. If you want to be anal about it, you can specify that Khabib dominated RDA solely on the ground, but that does not take away anything from his victory.