Update: this is live now — 1.4.0 shipped today, and your comment is the reason it exists.
Both of your ideas work in the editor now, no XML needed. ESC menu → Mining Layers → Layers: the pay seam is the fixed last row — pick COAL for your coal mine, LIMESTONE and STONE for the gravel pit (DIRT, SOIL, GRAVEL, SAND work too). PAYDIRT stays the default, and the bedrock at the bottom stays fixed — digging through the overburden to reach the goods is the point of the mod.
One catch: COAL and LIMESTONE are not base-game fill types — your map or a mining mod has to bring them (RGC maps like Yukon Back Country do). If the map doesn't know the material, the mod falls back to PAYDIRT and tells you in the log.
Thanks for the nudge — exactly the kind of feedback I need.