The Navmesh Issue (Patreon)

I remember the days when I used to make fun of modern games for requiring navigation meshes to work... and here I am now, suffering from bad karma.

Unfortunately, the current pipeline needed to create a hand-crafted level seems to be limited in regards to how much I can edit the navigation mesh...

So basically, I can generate it for the ENTIRE map at once, which also includes undesired parts like the top of the level geometry. Now, in order to solve this I have a few options:
a) Manually make the navmesh in Blender - extra dev time burden, but ultimately reliable;
b) Split the level in two different imports (one for navmesh and one for no-navmesh) - more automated but adds up to the already overly complicated level making pipeline;

c) Just leave it as it is - I am not yet sure of the implications of working with the messy auto-generated navmesh. Needs further investigation.

I don't think I can come up with an answer now, so this adds to the trials and errors of finding what works best for the game, but I figured I'd share the current state of affairs with you guys.