Spatial Shader ALPHA makes mesh draw over NavigationMesh3D nav mesh and other visual nodes

### Tested versions

- Reproducible in 4.3.stable

### System information

Windows 10 64 bit - Godot 4.3.stable - Vulkan (Forward+)

### Issue description

While APLHA is changed in the 3D mesh's shader, the mesh(es) with the shader will draw over other nodes, eg. NavigationRegion3D's nav mesh.

Here's what it looks like with ALPHA disabled:

and with ALPHA enabled:

### Steps to reproduce

- add NavigationRegion3D to scene
- Import a model from blender
- add collision to mesh (for navigation region 3D)
- Add a spatial shader with ALPHA set to 1.0 (as example) to the model

### Minimal reproduction project (MRP)

[example-project.zip](https://github.com/user-attachments/files/17388928/example-project.zip)

Start with the attached example-project.zip and reproduce the issue in Godot 4.3.stable using Vulkan Forward+. Compare the spatial shader with ALPHA disabled and enabled, then trace the 3D rendering interaction between the model and NavigationRegion3D's navigation mesh. Done means the model no longer draws incorrectly over the navigation mesh and other visual nodes when ALPHA is used.

Written by the indexing model from the issue text.