How to deal with the edge tile

As of the current version of Dwarf Fortress, Dwarves and Adventurers do not stack things. Ever.

If the bolts are metal, it might be better to melt them down instead so that you will eventually recoup some of the metal for a new stack, because the alternative, as you yourself mention, is a dwarf running around with a 1 stack of ammunition.

So I just tested this out myself -- you've made a mistake, albeit a small one.

You're correct that building an upward staircase won't reveal the tile -- you're wrong that the tile can't be reached for digging a down staircase (or up/down in my case). Just designate the tile directly above the constructed staircase, as normal, and soon enough, one of your miners will come along and take care of it.

The big difference here is that because the tile is not revealed, it will not flash when a miner is pathing to perform the dig job. I'm betting this is why you thought it wasn't working? However, the job still exists, and will be performed normally.