### Godot version

4.1.beta3

### System information

Godot v4.1.beta3 - macOS 13.2.1 - Vulkan (Forward+) - dedicated AMD Radeon Pro 580 - Intel(R) Core(TM) i7-7700K CPU @ 4.20GHz (8 Threads)

### Issue description

When baking the mesh in GDScript after placing a Node3D (StaticBody3D with CollisionShape3D) these error message are displayed:

```
E 0:00:02:0733   update_polygons: Navigation map synchronization error. Attempted to update a navigation region with a navigation mesh that uses a different `cell_height` than the `cell_height` set on the navigation map.
  <C++ Source>   modules/navigation/nav_region.cpp:114 @ update_polygons()

E 0:00:19:0007   sync: Navigation map synchronization error. Attempted to merge a navigation mesh polygon edge with another already-merged edge. This is usually caused by crossing edges, overlapping polygons, or a mismatch of the NavigationMesh / NavigationPolygon baked 'cell_size' and navigation map 'cell_size'.
  <C++ Source>   modules/navigation/nav_map.cpp:770 @ sync()
```


**In Godot v4.1.beta2 it worked,** i.e. no error message

### Steps to reproduce

GDScript:
```
@onready var _navigationRegion3D: NavigationRegion3D = %NavigationRegion3D

:

_navigationRegion3D.bake_navigation_mesh(false)
```

Properties NavigationRegion3D:
<img width="434" alt="CleanShot 2023-06-22 at 19 15 44@2x" src="https://github.com/godotengine/godot/assets/1539838/30410b5f-99f1-40a4-82d4-2d6d66f673d5">


### Minimal reproduction project

[RTS 3D BakeIssue.zip](https://github.com/godotengine/godot/files/11839898/RTS.3D.BakeIssue.zip)

rcPolyMesh *poly_mesh = nullptr;
	rcPolyMeshDetail *detail_mesh = nullptr;
	rcContext ctx;
	
	String bake_state = "";
	bake_state = "Setting up Configuration..."; 
	const float *verts = vertices.ptr();
	const int nverts = vertices.size() / 3;
	const int *tris = indices.ptr();
	const int ntris = indices.size() / 3;
	float bmin[3], bmax[3];
	rcCalcBounds(verts, nverts, bmin, bmax);
	rcConfig cfg;
	memset(&cfg, 0, sizeof(cfg));
	cfg.cs = p_navigation_mesh->get_cell_size();
	cfg.ch = p_navigation_mesh->get_cell_height();
	cfg.walkableSlopeAngle = p_navigation_mesh->get_agent_max_slope();
	cfg.walkableHeight = (int)Math::ceil(p_navigation_mesh->get_agent_height() / cfg.ch);
	cfg.walkableClimb = (int)Math::floor(p_navigation_mesh->get_agent_max_climb() / cfg.ch);
	cfg.walkableRadius = (int)Math::ceil(p_navigation_mesh->get_agent_radius() / cfg.cs);
	cfg.maxEdgeLen = (int)(p_navigation_mesh->get_edge_max_length() / p_navigation_mesh->get_cell_size());
	cfg.maxSimplificationError = p_navigation_mesh->get_edge_max_error();
	cfg.minRegionArea = (int)(p_navigation_mesh->get_region_min_size() * p_navigation_mesh->get_region_min_size());
	cfg.mergeRegionArea = (int)(p_navigation_mesh->get_region_merge_size() * p_navigation_mesh->get_region_merge_size());
	cfg.maxVertsPerPoly = (int)p_navigation_mesh->get_vertices_per_polygon();
	cfg.detailSampleDist = MAX(p_navigation_mesh->get_cell_size() * p_navigation_mesh->get_detail_sample_distance(), 0.1f);
	cfg.detailSampleMaxError = p_navigation_mesh->get_cell_height() * p_navigation_mesh->get_detail_sample_max_error();
	if (!Math::is_equal_approx((float)cfg.walkableHeight * cfg.ch, p_navigation_mesh->get_agent_height())) {
		WARN_PRINT("Property agent_height is ceiled to cell_height voxel units and loses precision.");
	}