Yes, for some adjustments, a seatstay can be bowed which will lift the corresponding dropout. But it's hard to do without being visible. But I'll answer the question with one of my own. Why not file it?

The best solution is the simplest, filing the top of the slot, both for vertical and horizontal dropouts. The next best solution, or actually just as good is to fill the high dropout by the same amount. This should be done with something with a bit of structural strength such as a bit of shim stock at the top, and JB Weld or similar to hold it all together.

I've done it this way in the past using shim stock and body filler and it held up very well, but since it'll need filing anyway I prefer to cut to the chase and file the low side higher. There's plenty of meat on a dropout and removing 1/32" or so has no negative consequence. Also, fill can break down, or fail to bond well, whereas a filed surface is every bet as good as the original.

BTW- if you have an expensive custom built frame, there's a fair chance that this was already done to super precisely dial in the wheels position.