Third brake light spoiler installation issue

Could you take a picture of the assembly and show where the issue is? The light itself or the trim panel won't go back into place around it. If it's the lamp check that the grommet is fully seated, and the wiring isn't bunched. If it's the trim panel check that the clips at the front are inserting fully. It doesn't take much to keep them from snapping into place.
In theory they can't pull you over if the CHMSL was missing because most places only require at least two brake lights be working. However, those laws are always getting changed and if they are hunting for tickets, you would have a lamp out. Now if you were asking if you could drive it while you were repairing it, toss the parts in the back to show them if you are stopped. However, be sure to cover the hole for the wiring to keep water out.

It's the trim panel, when I put the clips on the pin, it won't sit flush against the window and the screw holes don't line up.

Check the outer tab alignment on the outer edges. I've seen them bend enough that the trim won't move all the way to the body and seat properly. I've also seen the clips get distorted enough that they hold it away.