I have never seen any "borate dust" per se in the air when milling, but if it is there (and it probably is) then it's mixed in with the fine sawdust, and you are going to avoid breathing THAT anyway. The main thing is, in my limited experience, I have not seen lumber treated with the glycol solution cause any problems with finishing.
Must you coat it all? I have no idea. It's certainly a good idea to spray from the top, not the sides, so that gravity helps, though I don't know for certain that this is necessary. Maybe you could just continuously spray from the top of the pile for a long time, figuring the solution will pass through each board & eventually get to the bottom ones? That would probably be very wasteful, though, and the stuff ' aint cheap.
I coated all of my boards on all surfaces, because I had a pretty large problem. (I lost several thousand BF !) What I did was skip plane all 4 surfaces, so I could look for holes and trails, then cut-away the obviously infected sections. THEN I sprayed it all down.
I needed to rebuild my stacks anyway, (Get tarps underneath, and design-in more air flow.) so for me this was a no-brainer.