Originally, the stud portion was part of the frankenstein bolt, not captive to the body. It's R1-38X in this drawing:
This is because not all cars came with the fastening points for the hard-top. If you car was ordered without the hard-top, it might have simply come with two screws in each plate, rather than one screw and one stud/frankensetin:
For vehicle so equipped, the dealer would remove one R1-382 screw on each side, and replace it with the R1-38X for customers who ordered a hard-top as an accessory.
(I'm not sure why some non-hardtop cars got the 38X bolt anyway. My '92 came with 'em, despite the fact that it didn't have the side striker plates for the hardtop latch.)
That said, when I have unscrewed these in the past (such as to paint the car), the stud has always remained in place. When new, it came with some threadlocking compound already applied, such that it's not going to budge easily:
If you absolutely need to get it out, try the double-nut method. Go out and buy two thin hex nuts that fit the stud, and lock them together. Then use a wrench on the lower one to pull the stud out.
If that doesn't work, just go to the dealer and order two of p/n NA01-R1-38XB. Rosenthal has them for $17.13 each: REAR DECK STUD (NA01-R1-38XB) - $17.13 - NA01R138XB