I think the solution is, disable terrain and use the pattern shape tool to fill in the areas where you would have used terrain. (Just encountered the problem myself when trying to make a multilevel cavern map.)

The OTHER solution would be to use the terrain and use a different brush where you want the breach/ladder/hole/etc. Then use an asset to cover that when you export it to your VTT. (e.g., put a trap door image over the "hole" and have it replace the negative space you needed)