### 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)

if (!Math::is_equal_approx((float)cfg.walkableClimb * cfg.ch, p_navigation_mesh->get_agent_max_climb())) {
		WARN_PRINT("Property agent_max_climb is floored to cell_height voxel units and loses precision.");
	}
	if (!Math::is_equal_approx((float)cfg.walkableRadius * cfg.cs, p_navigation_mesh->get_agent_radius())) {
		WARN_PRINT("Property agent_radius is ceiled to cell_size voxel units and loses precision.");
	}
	if (!Math::is_equal_approx((float)cfg.maxEdgeLen * cfg.cs, p_navigation_mesh->get_edge_max_length())) {
		WARN_PRINT("Property edge_max_length is rounded to cell_size voxel units and loses precision.");
	}
	if (!Math::is_equal_approx((float)cfg.minRegionArea, p_navigation_mesh->get_region_min_size() * p_navigation_mesh->get_region_min_size())) {
		WARN_PRINT("Property region_min_size is converted to int and loses precision.");
	}
	if (!Math::is_equal_approx((float)cfg.mergeRegionArea, p_navigation_mesh->get_region_merge_size() * p_navigation_mesh->get_region_merge_size())) {
		WARN_PRINT("Property region_merge_size is converted to int and loses precision.");
	}
	if (!Math::is_equal_approx((float)cfg.maxVertsPerPoly, p_navigation_mesh->get_vertices_per_polygon())) {
		WARN_PRINT("Property vertices_per_polygon is converted to int and loses precision.");
	}
	if (p_navigation_mesh->get_cell_size() * p_navigation_mesh->get_detail_sample_distance() < 0.1f) {
		WARN_PRINT("Property detail_sample_distance is clamped to 0.1 world units as the resulting value from multiplying with cell_size is too low.");
	}
	cfg.bmin[0] = bmin[0];
	cfg.bmin[1] = bmin[1];
	cfg.bmin[2] = bmin[2];
	cfg.bmax[0] = bmax[0];
	cfg.bmax[1] = bmax[1];
	cfg.bmax[2] = bmax[2];
	AABB baking_aabb = p_navigation_mesh->get_filter_baking_aabb();
	if (baking_aabb.has_volume()) {
		Vector3 baking_aabb_offset = p_navigation_mesh->get_filter_baking_aabb_offset();