[Delphinus]

I just painted the insides of mine. I don't know what their reasoning is, but I found that painting an oil based white paint on my stand, ie., on bare wood, even with a proper primer as a first coat, it just sucked that paint right in. So it looked good after I first put it on, but then later it would almost look like bare wood in spots. This was the plywood part though.

I'm not sure I completely follow what you're saying about plywood over top of, but if I DO understand correctly, ie. that you are talking about painting the wood that will get covered by the plywood skirting, then I don't think you need to paint those parts excessively. It will be wood against wood and not really a spot that mildew is going to grow... I think anyhow.

You're not using particle board or OSB so it's not like the wood getting wet can lead to structural problems. In this case it's mainly for mildew control which I think means just do the areas that will be left exposed after you're finished building.