Thanks for the question. For the cap holes feature, we use a 3ds Max Meshes library available in its SDK and unfortunately we're limited by what that makes available to us. Specifically, there isn't any weld threshold parameter in the cap holes function, it's handled entirely by the Max meshes library.
When this has cropped up in the past, users have been able to use a smaller scene units option to get around the limitation.
I hope that helps,