After becoming a deity Makarov clearly felt the plane barriers for the first time, he could feel the vaugue plane will of his plane, it wasn't injured apparently from the collision it had experienced with another plane some time ago. It was at this point Makarov actually understood the origin of the ruins he had been to, confirming his suspicion that there were indeed other worlds out there.
Curiousity gripped at him, he wanted to see what other worlds were like and so ignoring the vaugue message from the nascent plane will he pierced through the planar barriers utilizing the laws he understood to pierce through the spatial barriers by temporarily transforming himself into the familiar light elemental particles an instinct he acquired with his breakthrough and the using the wave particle function ignored the barriers of the plane and came to the void.
