Metroids are described as energy beings, despite being somewhat obviously physical. They grow when they absorb energy, however. If one wants to equate life energy to souls, one could say that Metroids may have an excess of soul. Space Pirate data and experiments state that they can't find whatever it is Metroids drain, and have determined that it is not a physical thing. Might be souls, might not be.
Anyway, Phazon Metroids do indeed phase through matter and out of space-time. One of them could simply phase through the floor and attack Kain's crotch. It's impossible to detach a feeding Metroid without causing yourself to explode. Of course, there's something that hasn't been mentioned yet: Phazon Metroids can shoot lightning. Phazon enhanced lightning.
And this is in Skytown? Well, Elysia is sort of a gas giant planet, and the atmosphere is inhospitable to humans. I don't know how that will affect Kain, but I thoought it should be pointed out.