This is just to give you guys some information in case any of you encounter this issue.
After replacing my top, I noticed that whenever I attempt to open the top, the edges of the tonneau cover will hit the metal support arm (where the adjustment nut is) of the soft top. It was really bad and the paint started to chip off.
After countless attempts with the workshop to resolve this, we finally figured out this was due to the bungee cords. Specifically the 5th bow bungee cords.
In my case, the workshop adjusted the cord and managed to get enough tension for the roof to be pulled more upright with more clearance for the tonneau cover.
If the tension is not sufficient, your bungee cords have been stretched out and will need to be replaced.
The part numbers are:-
971F8-1ET0A
971F9-1ET0A
Replacing of the bungee cord can be found in the service manual RF, under the section "5TH BOW BUNGEE CORD"
Another thing I noticed after this was done was previously, when the roof was closing (when the 5th bow opens up to latch with the tonneau cover lock) there will be a loud sound (something like when you attempt to open a huge umbrella with force) when the cloth top stretches open. After the tension of bungee cord was done, I don't get that loud sound anymore.
All these while when I got the car, I thought that sound was normal but right now the top closes more gracefully too.
Hope this information will help out fellow roadsters owners!