The sheer idea Evenepoel would fake a mechanical in this situation is insanity.
In a different scenario, maybe, I could envision a situation where it could make sense to try this, but what in the world would he have gained by that here? He lost the 8 seconds in any case, and there's zero chance he would have lost any more than that by following the peloton.
Or let's say he would have lost 20 seconds, so the *** what? I don't understand how that thought would even enter anyone's head.
Anyway, terrible thing to happen to Roglic, whom I actually like quite a bit, great attack and then awful luck, but also 100% his own fault to crash there it must be said. Staying on your bike is necessary to win a race too. Doesn't put any askerisk on the eventual winner in my opinion, whether it's Remco or Mas or whoever.
I can imagine the following scenario. Evenepoel senses he has lost pressure in a tire, informs the team car via race radio, which tells him to pull over (you've got a flat). Remco is uneasy, as he doesn't know if the inside the 3k rule shall apply, but is reasured by the team car that it would so he obeys. In fact, he was lucky, for initially the inside the 3k rule was not applied and he lost the jersey to Roglic, but that was amended and everything worked out. But I don't believe he could have faked a flat in this situation for, as you suggest, no way he would have gambled his leadership on a whim and the race jury's application (or not) of a rule. The potential risk to loose significant time as opposed to being docked just 8 seconds, as surely would have been the case had he continued on a unflatted tires, makes any suspicion of a ruse on Remco's part patently insane.
The only thing that perplexes me, although it must be just an oversight, is why didn't Remco specify which tire flatted front or rear? Then I read that according to Oldmanish the race commissionaires were not shown Evenepoel's bike to verify the incident. If true, but I have not read this officially, then it is also strange and not helpful to allaying doubts cast by conspiracy theorists.
In any case, with a flat pulling over was the right tactical move. He spared himself further effort and risk of crash, which, as Roglic prooves, stranger things could have happened.