The JTAG and MMDC groups are single function pads, but they are shown as checked and grayed out because they do have pad control registers that the user could use to adjust the electrical characteristics of the pads, and code is required to initialize those pads.
The other single function pads/signals are shown without a checkbox because they have no IOMUXC registers associated with them and therefore no code needs to be generated to configure them. They are simply included for completeness so all signals for a module are represented even if they do not need IOMUXC configuration.
Hope that helps. Please feel free to ask any questions or report problems.
Best regards,
Chris