I'm not sure that's the case.
Ultimately, anything Mercedes did other than what it did would have resulted in ceding track position to Verstappen. We've seen eight times this season what the result of that is, including once in this very same race. It didn't want that to happen, precisely because it would have resulted in a championship being decided by stewarding decisions.
That meant they couldn't pit first under VSC, so Verstappen did and got a cheaper stop. Hamilton could have covered it off the next time round, but the VSC had ended and he would have lost four seconds (and track position) for the self-same stop.
The situation was the same under the full SC. Had Hamilton pitted not knowing how the race was going to end - under SC, a racing lap, or a red flag restart - he'd have ceded track position, so he couldn't. Verstappen could, did, and got a free stop.
As for how that played out, Masi made up a rule on the fly to allow Verstappen onto Hamilton's gearbox for one racing lap right after Horner told him that was exactly what they needed (one race after negotiating a red flag restart position with the same team, which was already extraordinary).
Knowing what we know now, I don't think we can assume that if Hamilton had stopped and ended up with two lapped cars between him and Verstappen, Masi would have done the same thing - especially if Horner was on the blower saying "We can't compromise safety for the sake of racing, Michael, come on." to keep the SC out, or keeping the lapped cars in place.