He can choose what body parts he phases, so maybe he leaves his feet in the corporeal realm?
This issue is too complicated for Kishi to have ever considered it in the first place 0_o. Chalk it up to Pnj.
The method for defeating Obito was based on the fact that he could not phase one part of his body without making his entire body intangible in the first place. So no, he doesn't control which body parts he phases, rather he makes his whole body intangible and any part contacted by a foreign entity is automatically taken to his other realm.