the shulker origin does not mine cobblestone at the same speed as other stone types.

I don't know if it's a bug or not but it happens to me too

This happens because "cobblestone" (including: mossy cobble, granite, diorite, andersite) Isn't "Natural stone". This can be fixed by downloading the 'extra origins' which includeds: Dwarf. which updates "Natural Stone" to cobble and such.