You could use the same argument to postulate the planet somehow spitting Khan back out at some point. No, it's more likely that the planet will reshape itself according to normal physics now, with the protomatter having been consumed by the original formation in the first place.
Agreed on that, I guess. Although the planet might have resurrected Khan at an earlier date already, assuming it formed at and from the very detonation of Genesis and thus caught Khan tightly in its matrix...
Perhaps the Genesis Planet
is Khan reborn, tearing itself up in anger and frustration?
I see the Mutara Nebula as having been so dense because it was already forming a new planetary system, with a star already in place. The Genesis device interfered with the formation, and the planet in question formed unstable because of the protomatter. Now that that process is complete, the system can go back to what it was doing in the first place, just hurried up a little because of the interference by the Genesis device.
It wouldn't suffice for Genesis to form a new star or expose it from within the nebula. The old one (The one which the Regula rock orbited - itself named Regula? Or Mutara? Or something else?) would have to disappear somehow, too!
The simpler explanation IMHO is that there is only one star, the original one.
And only one planet, the one formerly known as Regula. Genesis was supposed to transform existing lifeless worlds into living ones, after all, and its programming could not accommodate one byte more, so flexibility to deal with nebulae sounds unlikely.
Sure, the simulation describing the programmed-in capabilities shows the Genesis Torpedo basically hitting the surface of the targeted lifeless body, rather than the waves reaching that body from a distant detonation. But we do learn that distant detonations still will have the Genesis effect on our heroes, so why not on Regula?
(Since the Mutara nebula clearly is off to one side of the local star, separated from it by a few impulse-minutes of travel, I trust you didn't mean this local star was the one "already in place". But we could argue the local star is an active one, and has burped out the nebula very recently in cosmic terms, perhaps wiping the system clean of other targets of interest in the process and just leaving the solid core of a past gas giant of D class. Now
that would also explain why "D class" refers to an exo-Saturn in VOY "Emanations"!)
The oddball planet is one of the main attractions of the movie in any case, and IMHO succeeds quite nicely. Especially the glacier/lava lake/mountain range matte with the sunset and sunrise really serves its purpose.
Timo Saloniemi