Ehhhh ... I dunno. The spot where the Ford oval on the trunk of Frankenstang's '86 GT used to be has a few little holes where it looks like they either pushed on or were kinda riveted on. I know the oval on my Notch is held on there with something besides tape, because I tried to delete it when I repainted it a couple of years back and couldn't get the thing off without risking its destruction - the LX badge was just slapped on there from the factory with double-sided tape, like the 5.0 badges. The same deal applies to all Foxes - hatches, notches, and 'verts.
My guess for the reason of different attachments is that not all Foxes are LX's or 5.0's, but ALL of them have the Ford oval on them from the factory.
Only thing I can suggest is to either try sticking the clear part back on with some 3M Emblem Adhesive glue, or figure out a way to cleanly and safely remove that thing without destroying the finish in the process.
On a side note ... hey, Frankenstang. Y'know how you said the hatch on your Capri is supposed to be the original? I'm wondering again if they didn't swap that hatch from a 'Stang, also, because 1. the glass on a Capri hatch is WAY different, and 2. that Ford oval is pressed on. So, like, unless your Ex drilled the holes and riveted on the Ford oval (or just slapped it on with glue or something) and/or the Capri glass uses the same outer hatch frame as the Mustang glass, then the hatch probably isn't 100% original, after all ... which would also explain the sloppy hinges on top. Sorry to sidetrack, just a thought that occurred to me...