The NavigationObstacle is avoidance velocity only, it does nothing for the pathfinding that is affected by navigation mesh surface only.
See obstacle documentation that also mentions this in the first section. Using NavigationObstacles — Godot Engine (4.2) documentation in English
Note that this got changed in Godot 4.3 and the obstacle has an option to bake to the navigation mesh in that version. You still need to rebake your navigation mesh regardless.