I don't think it works like a normal venue gig, where as you say the headline act get a proper sound-check and leave their gear on stage, and the support acts have to squeeze in in front of that for their sets with minimal sound-team support.
From what I've seen the stage is cleared completely between acts, and the next act has been setting up on mobile platforms back-stage, so they wheel on the drums and amps etc. already mic'd up and line-checked, and plug them into multi-way connectors on stage ready to go. So each act gets an equal bite at the PA cherry. Although, that said, it often seems that the headline act gets a bigger interval from the sub-headliners in which to make sure everything is set up perfectly - Kanye had a full hour's interlude in which to plug in his mic and laptop, f'rinstance, whereas most acts get about 30mins
So the difference is probably down to how good each band's sound team is at setting up that quickly and optimising the particular space that they're dealing with for their band's sound