As long as there's no water running along the ground into the run.
Even just poop drying and crumbling down into the grael could become and issue.
Best to have some kind of organic bedding to help break down the poops.
If you dig a hole in dense soil that doesn't drain, then fill it with gravel or crusher run(also a kind of gravel), it might drain water running to the area but it still won't drain into the dense soil beynd it.
Gravel of any kind can hold poop and water to form a noxious brew.