Hi. The prefabs are meant to be replacements for tiles - it does make sense what you want, but adding that as a general feature will open up doors to unending amounts of confusion - eg. add a character prefab, and he moves but leaves behind another character tile, etc. Its easy enough to patch in though - but what you're wanting seems to be a temp thing to create these box colliders to build the navmesh?
tk2dTileMapMeshBuilder.cs -
bool skipPrefabs = editMode?false:true;
set it to false, and the render part of the prefabs will always be built.