### 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)

if (mesh->blend_shape_count > 0) {
		mi->blend_weights.resize(mesh->blend_shape_count);
		for (uint32_t i = 0; i < mi->blend_weights.size(); i++) {
			mi->blend_weights[i] = 0.0;
		}
	}
	MeshInstance::Surface s;
	if ((mesh->blend_shape_count > 0 || (mesh->surfaces[p_surface]->format & RS::ARRAY_FORMAT_BONES)) && mesh->surfaces[p_surface]->vertex_buffer_size > 0) {
		
		s.format_cache = mesh->surfaces[p_surface]->format;
		if ((s.format_cache & (1 << RS::ARRAY_VERTEX))) {
			if (s.format_cache & RS::ARRAY_FLAG_USE_2D_VERTICES) {
				s.vertex_size_cache = 2;
			} else {
				s.vertex_size_cache = 3;
			}
			s.vertex_stride_cache = sizeof(float) * s.vertex_size_cache;
		}
		if ((s.format_cache & (1 << RS::ARRAY_NORMAL))) {
			s.vertex_normal_offset_cache = s.vertex_stride_cache;
			s.vertex_stride_cache += sizeof(uint32_t) * 2;
		}
		if ((s.format_cache & (1 << RS::ARRAY_TANGENT))) {
			s.vertex_tangent_offset_cache = s.vertex_stride_cache;
			s.vertex_stride_cache += sizeof(uint32_t) * 2;
		}
		
		glGenBuffers(1, &s.vertex_buffer);
		glBindBuffer(GL_ARRAY_BUFFER, s.vertex_buffer);
		GLES3::Utilities::get_singleton()->buffer_allocate_data(GL_ARRAY_BUFFER, s.vertex_buffer, s.vertex_stride_cache * mesh->surfaces[p_surface]->vertex_count, nullptr, GL_DYNAMIC_DRAW, "MeshInstance vertex buffer");