### Godot version

v4.0.beta14.official [28a24639c]

### System information

Windows 10, OpenGL

### Issue description

Vulkan and Mobile:
![Godot_v4 0-beta14_win64_kEcRNiMfNJ](https://user-images.githubusercontent.com/7782218/213967627-8e8755d9-2fe2-43b3-b197-f9f2840b7580.gif)

OpenGL:
![Godot_v4 0-beta14_win64_MQ233TZuPq](https://user-images.githubusercontent.com/7782218/213967651-ae463a6f-c867-4312-bdf1-525e1d7def01.gif)

At first I thought it was related to `set_buffer()`, but it turned out that `set_instance_*` also work incorrectly.
Probably the custom information is also set incorrectly, but I haven't checked it yet.

### Steps to reproduce

* Open MRP
* In the editor, select `MeshInstance3D` node and change the `Count` property
* -- or --
* Start the project and move the slider

You can also switch the renderer to Vulkan and compare.

### Minimal reproduction project

[set_buffer().zip](https://github.com/godotengine/godot/files/10476834/set_buffer.zip)

Mesh *mesh = mesh_owner.get_or_null(p_mesh);
	ERR_FAIL_COND_V(!mesh, false);
	return mesh->blend_shape_count > 0 || (mesh->has_bone_weights && p_has_skeleton);
}
void MeshStorage::mesh_add_surface(RID p_mesh, const RS::SurfaceData &p_surface) {
	Mesh *mesh = mesh_owner.get_or_null(p_mesh);
	ERR_FAIL_COND(!mesh);
	ERR_FAIL_COND(mesh->surface_count == RS::MAX_MESH_SURFACES);
#ifdef DEBUG_ENABLED
	
	{
		uint32_t stride = 0;
		uint32_t attrib_stride = 0;
		uint32_t skin_stride = 0;
		for (int i = 0; i < RS::ARRAY_WEIGHTS; i++) {
			if ((p_surface.format & (1 << i))) {
				switch (i) {
					case RS::ARRAY_VERTEX: {
						if (p_surface.format & RS::ARRAY_FLAG_USE_2D_VERTICES) {
							stride += sizeof(float) * 2;
						} else {
							stride += sizeof(float) * 3;
						}
					} break;
					case RS::ARRAY_NORMAL: {
						stride += sizeof(uint16_t) * 2;
					} break;
					case RS::ARRAY_TANGENT: {
						stride += sizeof(uint16_t) * 2;
					} break;