I assume, that pre-FL and FL soft tops kind of fold into the same "volume", otherwise the clamshell would differ. So it should not make a difference for the hard top fitment.
Did you check, where the exactly the top sits on the soft top?
I had that impression, too... at first, but i proofed myself wrong.
I think, that the spot where the Top is sitting on (spin locks) needed to be reduced/trimmed to make the TOP sink to a "flush" state. I decided against doing that, as I don't want to weaken critical spots by reducing material.
You can ONLY get a REAL first impression on how the TOP sits, by installing the locks/latches and lock them in...you will see how MUCH that will sink the TOP. Additional the hatch puts a little weight on the back of the TOP as well.
All in all, my Top is not 100% flush, it sits ~5mm higher which is okay with me.
I trimmed my TOP sides, as I decided to keep the side covers where they are. That is what the manual says, as well as the seller and what some YouTube videos showed. It might work out for you to keep them untouched, you should try first.
Oh...and btw...that hard, plastic tube for the cables....THAT is useless and definitely conflicting with the soft top. I yanked it out...helped too, I think.
