I believe the point being made, and one that I find myself agreeing with, is that the Protean cannot selectively halt its boiling like that. It either is or is not doing so. I will allow that the text is ambiguous on that point.
But beyond that, we've seen him with a face while sleeping, so that would seem to pretty definitively preclude him from deliberately shapeshifting eyes. Likewise, "not actually having eyes" would go against the idea that nothing about the chosen monster actually contradicts his pre-selection appearances (to say nothing of stretching artistic license to its breaking point), so that option is out. That leaves "contrived coincidence" as the only explanation that isnt contradicted by something, which... admittedly, at least is actually possible, so it does have that going for it compared to the other explanations, but holy crap would that be unsatisfying to me personally.