Yes any shade can make each section not produce power. These large panels are set in three sections. There are bypass diodes so the unshaded sections can still produce power. If going with an over/under configuration consider running them in parallel. Bottom panel will add power when extended. Make sure the slide mechanism gives you plenty of reach to completely expose the lower panel even when the sun is at an angle.
What is the actual width of the platform? '8 wide RV can get two of those panels side by side. In which case I would mount them side by side in the rear. Again in parallel with one getting shade when the kayak is mounted.
As shown both panels will produce about nothing when the kayak is up.