Except that the pocket dimension resides in the center of the planet, when Lavos comes out to attack the planet it has exited its pocket dimension. And also, the amount of needed matierial to close that hole would be hard to reproduce. Thats why I say that the hole was closed by Lavos and the reformed mountain.
The pocket dimension does not technically "exist" anywhere in reality as we understand it. It exists parallel to reality in the world, but Lavos' power, or another highly significant source of energy is capable of pulling the two together. When the intersect, then the pocket dimension can manifest itself in "reality" and, more than likely, parts of our reality can manifest themself in the pocket dimension.
Secondly, Let us not forget that when Lavos first arrived on the planet, there was no deep hole, just a crater with a gate. This suggests that the second of impact, he phased into his pocket dimension. Rather than living inside the planet, he lived perpindicular to it, and probably not too far beneath the surface.
Lavos' reappearence in 1999 AD would have easily caused massive volcanic activity. This would of course have been centered over Lavos himself. Since phasing out of time seems to be almost a defensive reflex action for Lavos, it is plausible that if he felt at some point the Magma threatened him, that he would have faded out, and the magma would have formed around the outline of where the pocket dimension was. This could explain the rapid growth of the mountain.