### 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)

int bs_expected_size = expected_size * mesh->blend_shape_count;
		ERR_FAIL_COND_MSG(bs_expected_size != p_surface.blend_shape_data.size(), "Size of blend shape data provided (" + itos(p_surface.blend_shape_data.size()) + ") does not match expected (" + itos(bs_expected_size) + ")");
		int expected_attrib_size = attrib_stride * p_surface.vertex_count;
		ERR_FAIL_COND_MSG(expected_attrib_size != p_surface.attribute_data.size(), "Size of attribute data provided (" + itos(p_surface.attribute_data.size()) + ") does not match expected (" + itos(expected_attrib_size) + ")");
		if ((p_surface.format & RS::ARRAY_FORMAT_WEIGHTS) && (p_surface.format & RS::ARRAY_FORMAT_BONES)) {
			expected_size = skin_stride * p_surface.vertex_count;
			ERR_FAIL_COND_MSG(expected_size != p_surface.skin_data.size(), "Size of skin data provided (" + itos(p_surface.skin_data.size()) + ") does not match expected (" + itos(expected_size) + ")");
		}
	}
#endif
	Mesh::Surface *s = memnew(Mesh::Surface);
	s->format = p_surface.format;
	s->primitive = p_surface.primitive;
	if (p_surface.vertex_data.size()) {
		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, p_surface.vertex_data.size(), p_surface.vertex_data.ptr(), (s->format & RS::ARRAY_FLAG_USE_DYNAMIC_UPDATE) ? GL_DYNAMIC_DRAW : GL_STATIC_DRAW, "Mesh vertex buffer");
		s->vertex_buffer_size = p_surface.vertex_data.size();
	}
	if (p_surface.attribute_data.size()) {
		glGenBuffers(1, &s->attribute_buffer);
		glBindBuffer(GL_ARRAY_BUFFER, s->attribute_buffer);
		GLES3::Utilities::get_singleton()->buffer_allocate_data(GL_ARRAY_BUFFER, s->attribute_buffer, p_surface.attribute_data.size(), p_surface.attribute_data.ptr(), (s->format & RS::ARRAY_FLAG_USE_DYNAMIC_UPDATE) ? GL_DYNAMIC_DRAW : GL_STATIC_DRAW, "Mesh attribute buffer");
		s->attribute_buffer_size = p_surface.attribute_data.size();
	}
	if (p_surface.skin_data.size()) {
		glGenBuffers(1, &s->skin_buffer);
		glBindBuffer(GL_ARRAY_BUFFER, s->skin_buffer);
		GLES3::Utilities::get_singleton()->buffer_allocate_data(GL_ARRAY_BUFFER, s->skin_buffer, p_surface.skin_data.size(), p_surface.skin_data.ptr(), (s->format & RS::ARRAY_FLAG_USE_DYNAMIC_UPDATE) ? GL_DYNAMIC_DRAW : GL_STATIC_DRAW, "Mesh skin buffer");
		s->skin_buffer_size = p_surface.skin_data.size();