While we’re waiting for the re-made Bus Pirate cases, we found another factory for the next revision. I think for our scale it makes sense to remove the insert nuts. The nuts are hand placed so it’s labor intensive and tricky to schedule production.
Instead, I added a cavity to the bottom of the case for a standard nut. We thought it might be more painful to assemble, but we preferred it to fumbling with the gunked-up insert nuts.
The prototype hole was just a tad big for standard M3 nuts.
We also randomly bought some clear nylon nuts ($$$) that fit like a dream and look pretty sharp.