My Ambystomatids love burrowing under their water dish. I can't see flat rocks being any different than that as long as you have dirt supporting it. That is, I see you just putting the rock flat on the dirt, and them burrowing under it.
I would avoid any shale type rocks as they can seep impurities (like oil). Sandstone might be a little crumbly/rough. Slate will have sharp edges, but if you file these down smooth, it should be fine. Granite and other igneous rock is basically inert and will be fine, if you can find it in flat shapes. I have pieces of petrified wood I found on the beach. Not quite 'natural', but still they look way cool!
Boil if you feel necessary, don't bake. Baking rocks that contain any moisture can cause them to explode. I just scrubbed mine well with a nylon brush.