Yeah; pregenerated navigation meshes aren't the greatest -- I would've honestly preferred it if Valve didn't bother generating any.
If you'd like to learn how to modify navigation meshes, I usually point towards
this Steam guide. I used their meshes back when SUF / Facepunch was around; not sure where to get them now.
Specifically for Wutville, you'll want to select the areas near BLU forward spawn and mark them as either
TF_MARK DOOR_NEVER_BLOCKS or
TF_MARK UNBLOCKABLE. The spawn door is marked as blocked after first cap.