In a word, yes.
The factory original tops on our '74 & '75 had buttons on the outside that matched the tonneau so it could be snapped in place over the lowered soft top. These were unique to each car as we could not switch the tonneaus between vehicles. At least we knew which one went where.
I will never be able to explain this correctly . . . . . The top was attached to a stretcher bar (my term) that was attached to the rear deck. A male snap was fixed to the exterior of the soft top for the tonneau. The rear deck of the car also had male studs affixed so the tonneau could be attached without the soft top in place.
So, the soft top could be installed, and then lowered with the spreader bar left fixed and the tonneau installed over the soft top. OR, the soft top could be completely removed and the tonneau installed using the rear deck snaps which were located in the same place as the studs on the exterior of the soft top.
Now that I have cloudied the waters, I will add that I do not have a clue what the new aftermarket tops and tonneau's are like! I would think that you might have to get the top & toneau from the same company at the same time to make everything align. Then again, you could simply install new snaps in the soft top for the tonneau to attach to.
Like I said, in a word, yes.