as he is poised to rule benevolently over the Hollow Earth. Having freed both Shimo and the Great Apes of the Subterranean Realm,he has earned the genuine respect and admiration of other Titans, even if he doesn't have the true physical/psychological dominance that the Alpha Titan typically...
(enhanced clone of the Earth's most powerful defendor). So making Mechagodzilla alien-made too after all that in the first season would've been too much, and making him part of the folly of man theme of season 2 helped the plot a lot like with the weapon testing accidental...