### 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)

MultiMesh *multimesh = multimesh_owner.get_or_null(p_multimesh);
	ERR_FAIL_COND_V(!multimesh, 0);
	return multimesh->visible_instances;
}
void MeshStorage::_update_dirty_multimeshes() {
	while (multimesh_dirty_list) {
		MultiMesh *multimesh = multimesh_dirty_list;
		if (multimesh->data_cache.size()) { 
			const float *data = multimesh->data_cache.ptr();
			uint32_t visible_instances = multimesh->visible_instances >= 0 ? multimesh->visible_instances : multimesh->instances;
			if (multimesh->data_cache_used_dirty_regions) {
				uint32_t data_cache_dirty_region_count = (multimesh->instances - 1) / MULTIMESH_DIRTY_REGION_SIZE + 1;
				uint32_t visible_region_count = visible_instances == 0 ? 0 : (visible_instances - 1) / MULTIMESH_DIRTY_REGION_SIZE + 1;
				GLint region_size = multimesh->stride_cache * MULTIMESH_DIRTY_REGION_SIZE * sizeof(float);
				if (multimesh->data_cache_used_dirty_regions > 32 || multimesh->data_cache_used_dirty_regions > visible_region_count / 2) {
					
					glBindBuffer(GL_ARRAY_BUFFER, multimesh->buffer);
					glBufferSubData(GL_ARRAY_BUFFER, 0, MIN(visible_region_count * region_size, multimesh->instances * multimesh->stride_cache * sizeof(float)), data);
					glBindBuffer(GL_ARRAY_BUFFER, 0);
				} else {