The difference between Watterson and Munroe is that Watterson made far more money but didn't have a ton of control, whereas Munroe probably makes less money but has far more control. Part of that is down to sheer popularity. Watterson is worth several hundred million dollars according to reports, whereas Munroe likely makes at most a few hundred k a year. Which is still very respectable, but not quite in the "fuck it, I'm retiring" impulse zone as Watterson's wealth is. Also, Watterson was fairly disconnected from his fans and the primary interaction of his work were the ongoing struggles with his syndicate masters. Whereas Munroe's main interaction related to his work is directly with his fans, which also directly provide his income (through merch sales, mostly).

So there's very much less reason for Munroe to get frustrated with the process and stop. Watterson got tired of the bullshit and decided he'd had enough. If Munroe gets bored of doing the strip I suspect he'll just move on to some other project, which will be equally public (like what-if).