if you want to tape it off, you can. remember that the paint ends where the tape starts. that means that your paints edge is right there, open to all car washes, all weather... and will start to flake off there without fail. a good prep will mean that it wont come off in sheets like yours is now, but it WILL peel there.
Now wouldn't the world be a better place if only you could put that edge up under the window, about an inch or so? a place that will never see the elements and NEVER peel. once assembled, the clear would flow smoothly under the rubber and the angels would sing. it would $uck to pay to fix it only for it to happen again.
Does it strike you odd that this peeling I speak of has already happened to you once? Looks like the last guy taped it off. Might wanna check the other side.
the clear is gonna cover the entire panel, so dont tape the light or roof trim off either. the rear glass gets a special tape that pulls the rubber back to allow the edge to flow under the rubber. you can leave the molding, I did on my own car. you just cant ever decide that you want it off because it'll leave this thick ring.
And you might want to blend the door cause fresh green where the qtr starts will most likely look out of place. but again, you dont have to. that would involve taking off the belt molding, handle, window frame, trim panel and the mirror
But I think I'm the one who told you this last time, and you're here looking for a second opinion, so I'll shut up now so that others might chime in.
It just boils down to right way-wrong way. and in a body shop, prep time =$. Save yourself the dough, and remove the glass, taillight, and roof trim yourself. That'll probably save 3.5 hrs cost for you, and get you a better job. a good deal if you ask me. Too bad you dont live up here, I'd fix it cheap.
Good luck with it though