The CJ top will fit the YJ. The rub is in the liftgate. The tailgate swing door fits under the liftgate. If the CHMSL and the spare are on the tailgate, they will interfere with the closing of the liftgate. They can both be closed, with some fidgeting, namely carefully closing both at the same time. In my opinion, this negates easy access to the rear storage area as getting the thing open is a pain in the neck (or other parts of the anatomy).
For what it's worth, I've seen plenty of them on YJs. They generally remove the spare tire from the tailgate.
As far as the original question, the top fits just fine. Might want to get longer attach bolts, depending upon gasket installation.
Hope this helps.