I used butyl tape to seal the holes when I drilled the roof of my Astro Van to add a rack to hold my solar panels.
I drilled the holes, cleaned the area with alcohol, put down the tape, and then bolted down the rack on top. It has been leak free for 6 years now. If you are leaving your factor rack off use a bolt and washer to fill the hole and provide for a solid cover over the tape.
https://www.homedepot.com/p/Dicor-Bu...34-5/310964213