### 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)

cfg.bmin[0] = baking_aabb.position[0] + baking_aabb_offset.x;
		cfg.bmin[1] = baking_aabb.position[1] + baking_aabb_offset.y;
		cfg.bmin[2] = baking_aabb.position[2] + baking_aabb_offset.z;
		cfg.bmax[0] = cfg.bmin[0] + baking_aabb.size[0];
		cfg.bmax[1] = cfg.bmin[1] + baking_aabb.size[1];
		cfg.bmax[2] = cfg.bmin[2] + baking_aabb.size[2];
	}
	bake_state = "Calculating grid size..."; 
	rcCalcGridSize(cfg.bmin, cfg.bmax, cfg.cs, &cfg.width, &cfg.height);
	
	if ((cfg.width * cfg.height) > 30000000) {
		WARN_PRINT("NavigationMesh baking process will likely fail."
				   "\nSource geometry is suspiciously big for the current Cell Size and Cell Height in the NavMesh Resource bake settings."
				   "\nIf baking does not fail, the resulting NavigationMesh will create serious pathfinding performance issues."
				   "\nIt is advised to increase Cell Size and/or Cell Height in the NavMesh Resource bake settings or reduce the size / scale of the source geometry.");
	}
	bake_state = "Creating heightfield..."; 
	hf = rcAllocHeightfield();
	ERR_FAIL_COND(!hf);
	ERR_FAIL_COND(!rcCreateHeightfield(&ctx, *hf, cfg.width, cfg.height, cfg.bmin, cfg.bmax, cfg.cs, cfg.ch));
	bake_state = "Marking walkable triangles..."; 
	{
		Vector<unsigned char> tri_areas;
		tri_areas.resize(ntris);
		ERR_FAIL_COND(tri_areas.size() == 0);
		memset(tri_areas.ptrw(), 0, ntris * sizeof(unsigned char));
		rcMarkWalkableTriangles(&ctx, cfg.walkableSlopeAngle, verts, nverts, tris, ntris, tri_areas.ptrw());
		ERR_FAIL_COND(!rcRasterizeTriangles(&ctx, verts, nverts, tris, tri_areas.ptr(), ntris, *hf, cfg.walkableClimb));
	}
	if (p_navigation_mesh->get_filter_low_hanging_obstacles()) {