### 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)

s->bone_aabbs = p_surface.bone_aabbs; 
	if (p_surface.skin_data.size() || mesh->blend_shape_count > 0) {
		
		int size = p_surface.vertex_data.size();
		int vertex_size = 0;
		int stride = 0;
		int normal_offset = 0;
		int tangent_offset = 0;
		if ((p_surface.format & (1 << RS::ARRAY_VERTEX))) {
			if (p_surface.format & RS::ARRAY_FLAG_USE_2D_VERTICES) {
				vertex_size = 2;
			} else {
				vertex_size = 3;
			}
			stride = sizeof(float) * vertex_size;
		}
		if ((p_surface.format & (1 << RS::ARRAY_NORMAL))) {
			normal_offset = stride;
			stride += sizeof(uint16_t) * 2;
		}
		if ((p_surface.format & (1 << RS::ARRAY_TANGENT))) {
			tangent_offset = stride;
			stride += sizeof(uint16_t) * 2;
		}
		if (mesh->blend_shape_count > 0) {
			
			s->blend_shapes = memnew_arr(Mesh::Surface::BlendShape, mesh->blend_shape_count);
			for (uint32_t i = 0; i < mesh->blend_shape_count; i++) {
				glGenVertexArrays(1, &s->blend_shapes[i].vertex_array);
				glBindVertexArray(s->blend_shapes[i].vertex_array);