### 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)

rcFilterLowHangingWalkableObstacles(&ctx, cfg.walkableClimb, *hf);
	}
	if (p_navigation_mesh->get_filter_ledge_spans()) {
		rcFilterLedgeSpans(&ctx, cfg.walkableHeight, cfg.walkableClimb, *hf);
	}
	if (p_navigation_mesh->get_filter_walkable_low_height_spans()) {
		rcFilterWalkableLowHeightSpans(&ctx, cfg.walkableHeight, *hf);
	}
	bake_state = "Constructing compact heightfield..."; 
	chf = rcAllocCompactHeightfield();
	ERR_FAIL_COND(!chf);
	ERR_FAIL_COND(!rcBuildCompactHeightfield(&ctx, cfg.walkableHeight, cfg.walkableClimb, *hf, *chf));
	rcFreeHeightField(hf);
	hf = nullptr;
	bake_state = "Eroding walkable area..."; 
	ERR_FAIL_COND(!rcErodeWalkableArea(&ctx, cfg.walkableRadius, *chf));
	bake_state = "Partitioning..."; 
	if (p_navigation_mesh->get_sample_partition_type() == NavigationMesh::SAMPLE_PARTITION_WATERSHED) {
		ERR_FAIL_COND(!rcBuildDistanceField(&ctx, *chf));
		ERR_FAIL_COND(!rcBuildRegions(&ctx, *chf, 0, cfg.minRegionArea, cfg.mergeRegionArea));
	} else if (p_navigation_mesh->get_sample_partition_type() == NavigationMesh::SAMPLE_PARTITION_MONOTONE) {
		ERR_FAIL_COND(!rcBuildRegionsMonotone(&ctx, *chf, 0, cfg.minRegionArea, cfg.mergeRegionArea));
	} else {
		ERR_FAIL_COND(!rcBuildLayerRegions(&ctx, *chf, 0, cfg.minRegionArea));
	}
	bake_state = "Creating contours..."; 
	cset = rcAllocContourSet();
	ERR_FAIL_COND(!cset);
	ERR_FAIL_COND(!rcBuildContours(&ctx, *chf, cfg.maxSimplificationError, cfg.maxEdgeLen, *cset));
	bake_state = "Creating polymesh...";