Will these caps work with a tonneau cover or bed cover?

These are designed for the factory rail itself. If your tonneau cover clamps directly to the rails, test-fit before finalizing installation to confirm clearance.

Do I need fasteners beyond what's included?

The caps use factory mounting points on the rails. Confirm what hardware comes in the box, and have standard hand tools on hand—you may need fasteners that aren't included depending on your rail configuration.

Can I paint or seal these before installation?

Paint them before installing if you want a finished look. Let any coating fully cure, then mount. Masking tape on the mounting surfaces keeps adhesive or fasteners from sticking to paint.