Well, that's a new one on me!
It' looks as though the side screws are under a rubrail rubber, Y/N?
As for the spacing for the side I'd still stick with the 4" providing they go all the way thru. On the top I guess one would have to make that judgement for them self depending on the thickness of the material. Rubrails go any where from 2-6" depending on the manufacture.
Also, since your getting water in there, I'd lay a good bead of sealer under that corner of the toerail and let it ooz out when you tighten it down.
Is this picture above your actual system????