For that, I can understand some of the effects being done in AE.
From my experience, this sort of project comes in with a lot of clips, maybe different cameras or not, but often with different lighting & scene setups. It's typical to do the basic cutting together of the sequence as the first job ... when you've got your cuts & transitions & fades & such right to the beat. Then is when one starts working the AfterEffects and colorist things. You're only working the media you're actually using ... and pretty much all clips are where they're going to stay.
Any effects you add, do so in Adjustment layers above the media tracks as often as you can. Then you can turn them on/off as you need both for viewing ... (on) ... and for playback and checking of other effects ... (off). Give your tracks colors that mean something ... say media is the standard magenta, AE comps are blue, that sort of thing. Makes it easier to sort out what you've got going on ... when & where.
Any Looks you're going to apply to the whole project are especially best done in adjustment layers up above everything. Well ... normally above everything. Occasionally there's even stuff that gets added and it's easier to just go up top with another track.
There are times I'll essentially grade first ... but that's only when I've got a clip or two that will be the entire project, and I might as well grade them each before cutting them up ... using a Master Clip effect.
Jim shoots The Traditional 23.976, I shoot 29.97 ... music vids can be all over the place I know ... especially if the camera people start consuming what the band & performers & roadies are consuming ... sheesh ... 
Neil