It's all 3/32" balsa sheets. I finished the sanding at 320 grit, did two coats of thinned nitrate then two coats of thinned sanding sealer. I've been thinking the same way as you I believe. I feel like the wood wasn't fully sealed and the grain swelled, making small low spots where the primer filled. I intend to use the silver as my undercoat, which is why I'm doing both.
I think I get what you mean though, the thinner is soaking in to the wood, raising the grain, and the tissue is pulled deeper into the new valleys leaving the pits. What gets me is that the silver isn't filling in the pits when I spray (50-50 blend). In other words, if I sand off the silver, I'd expect the pits to either still be silvered, having been untouched by the sanding, or sanded away.
I think what I'll do is spray the silver, wet sand it down until it starts thinning out, and spray the silver again. Try to build it up without sanding it all away. I can also check the viscosity of the dope I'm spraying to see if I'm reducing too much but I haven't had the impression that it's the case.