Turns out this was an issue with the PDF form I imported. It allowed me to configure the checkbox fields on import, but they didn’t actually check on submission. The completed form was still clickable, so I don’t know what is up with that. I deleted the existing checkboxes, and created them in the plugin gui, and the submission checks work as expected.
Yes, I do. I’m not sure if some are just not listed and need to be added as custom capabilities though.