There is actually no reason why Zant should be able to get out and not Ganondorf. There is no seal on the TR apart from it naturally being another dimension. If Zant can use the ToP to defend against the light, so could Ganondorf...

Ok, I've come up with a possibility. When the interlopers entered the TR, the became spirits like Ganondorf. After being there for a longer period than Ganondorf, the interlopers developed bodies as the became acclimated to the TR. Zant had a body so he could be sent outside, but Ganondorf didn't. As the twilight took over Hyrule, Ganondorf entered this twilight Hyrule which in a sense was between the worlds of light and twilight. In twilit Hyrule, the twilight's effects were lessened and hie was exposed to his native light. In those conditions he could acquire a body much faster. As long as he reached the point where he could survive in the light before the twilight completely disappeared, he could complete his body while in the world of light.

Either that or he lived inside Zant. Yeah, that. It's simpler. I forgot that's actually what happens.