The Melbourne Volkswagen factory sealed and painted inside the tunnel when the car was built, by using a full-dip prep and paint process, the first of its kind in Australia.
The only things that could affect this, all these years later, would be if you had your pan acid-dipped (which would remove the VW paint). Welding on new floor sections would also destroy part of the original paint where the heat transfers across.
Yes Dave's suggestion about running down the tunnel (until it drips out) is probably best. You could also use Lanotec
http://www.lanotec.com.au/?link=3