NavigationRegion3D with multiple floor levels bakes polygons with wrong height

### Tested versions

- Reproducible in: 4.3.rc1, 4.2.2.stable

### System information

Linux - Godot v4.3.rc1.official.e343dbbcc - Vulkan (Forward+)

### Issue description

With specific geometry, like map with bridges or multiple connected height levels (floors), NavigationRegion3D may create polygons using height from wrong level.
Current example bugs with sample_partition_type `Monotone` or `Layers`

### Steps to reproduce

1. Open MRP
2. Select NavigationRegion3D node
3. Click `Clear NavigationMesh`
4. Click `Bake NavigationMesh`

### Minimal reproduction project (MRP)

[nav-bake-3d.zip](https://github.com/user-attachments/files/16459379/nav-bake-3d.zip)