I wanna remove the stock roof rack completely. What is the best way to seal the mounting holes off permanently?

 

weld, but it a lot of work. a urethane chaulking should be fine if you are not concerned about looks , otherwise weld, grind, paint. or put a nice shiny stainless steel button head screw there with a rubber gasket or chaulking under the head. You can paint the screw head if you desire, in which case you wont need to use stainless.

 

you mean caulking ? or gasket maker ??