Create a constant 5 mm gap between decking and side panels
I've always just held the decking back from the skirt (which is fastened tight to framing) to create a gap, but this obviously results in an undrained channel. I can see the benefit of your plan for allowing small tree debris and other dirt to drop out. 

Rip some 5mm strips of your decking material from scrap and cut them just shorter than the height of the skirt (so they don't show). Skip the glue (too slow and messy) and just tack them on at 16" intervals (or in line with your joists) with small galvanized nails. Screw on your skirt boards and be happy. 

One thing to keep in mind, though: Unless you don't fasten your decking to the rim joist, expansion pushes the framing also, making your gap useless. In my experience, decking doesn't move enough to warrant such a gap. It may be nice to have it for aesthetic reasons, though. Sometimes flush butt joints are ugly.