I'm sorry, Petrus, but this is my mission. That is to smite any fool who would deny the power of The Beyonder. And Lord of the Myths, I'm sorry for having to destroy your love for Lovecraft Lore. I once believed, as you did, that they were supreme. But alas, the tip-top Marvel and DC beasts like The Presence, Mxy, Beyonder, Molecule Man, etc are beyond even Yoggy and Nya. 🙁
1. I think it's funny that you mention how in Lovecraft Lore, our universe is insignificant to the Outer Gods. The entire transfinite Marvel Multiverse was similarly insignificant to The Beyonder, to the extent that it was compared to man discovering germs for the first time. And yes, Yog Sothoth cannot enter standard space without the Necronomicon and the knowledge of a man to summon him. You're assuming Lovecraft Lore is subject to some feats war where if some, "random hocus pocus spell" can allow Yog to enter space, surely he can do it of his own volition. Except that there isn't even the slightest indication of that being the case. And if your argument is that he doesn't care, then summoning Yog Sothoth wouldn't work anyways. It hardly contradicts Lovecraft's notion that Yog is limitless, it's just that he's barred from going into conventional space, most likely due to the fact that he's limitless. Nevertheless, that's a restriction The Beyonder doesn't have, who himself was a limitless being in the exact same way Yog Sothoth was, and was able to transform into a 3-Dimensional being and enter the Marvel Totality.
I'd argue that it doesn't imply comparable power, like at all. The daemons beat the monotone drums and blow the idiot flutes to soothe Azathoth, to keep him asleep. It has absolutely nothing to do with some comic-like conception of power. It remains fact that Azathoth is the creator of Yog Sothoth's creator, and in turn everything else in Lovecraft's lore, is but Azathoth's dream. When he wakes up, he'll be alone again. Like, his mere awakening will cause Yog Sothoth to simply...not exist anymore. As such, regardless of his unparalleled idiocy, Azathoth is the only truly all-powerful being in Lovecraft Lore, and nothing else compares. The only reason Yog Sothoth is considered the supreme archetype is because he's the strongest Outer God not named Azathoth, who's a complete and utter blind idiot god, and in turn...not really much of an archetype.
2. Except you have no evidence that there's an infinite number of multiverses involved, but rather a single Hilbert space-time globule. Also, you recall wrong, even the Molecule Man is a relative ant compared to the Beyonder at his full power, (note: at his full power. The Beyonder held back throughout all of Secret Wars). The Molecule Man literally compares The Beyonder's superiority to him to his own superiority over Captain-Freaking-America:
This Owen who's far more powerful than all the Marvel Cosmic entities combined, and can repair Multiverse-wide destruction in mere seconds.
The reason Marvel will always beat Lovecraft is two reasons: Versatility and context for power. Yog Sothoth doesn't possess nearly the breadth of abilities a being like The Beyonder has, who already possesses Godlike/Nigh-Omnipotent abilities like Causality and Acausality, along with the litany of Marvel energy attacks, (but just on a scale where he could, say, blow up the multiverse with his finger,) and other haxx abilities:
Yog Sothoth, conversely, has never even been in a fight, and we don't really have much context for how he even would fight. All we really have from him is his speaking being compared to universes converging onto one point to destroy it. Not only is that completely and utterly insignificant compared to what The Beyonder can dish out, but it's very flowery and hyperbolic in nature, (such as the various accolades calling Odin and Galactus omnipotent). As such, I'm definitely taking The Beyonder in a fight, whether it's the lack of restraint on his abilities, his versatility, or the context for which his Nigh-Omnipotence can affect a fight.