### 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)

}
void MeshStorage::update_mesh_instances() {
	if (dirty_mesh_instance_arrays.first() == nullptr) {
		return; 
	}
	glEnable(GL_RASTERIZER_DISCARD);
	
	while (dirty_mesh_instance_arrays.first()) {
		MeshInstance *mi = dirty_mesh_instance_arrays.first()->self();
		Skeleton *sk = skeleton_owner.get_or_null(mi->skeleton);
		
		float base_weight = 1.0;
		if (mi->mesh->blend_shape_count && mi->mesh->blend_shape_mode == RS::BLEND_SHAPE_MODE_NORMALIZED) {
			for (uint32_t i = 0; i < mi->mesh->blend_shape_count; i++) {
				base_weight -= mi->blend_weights[i];
			}
		}
		for (uint32_t i = 0; i < mi->surfaces.size(); i++) {
			if (mi->surfaces[i].vertex_buffer == 0 || mi->mesh->surfaces[i]->skeleton_vertex_array == 0) {
				continue;
			}
			bool array_is_2d = mi->surfaces[i].format_cache & RS::ARRAY_FLAG_USE_2D_VERTICES;
			bool can_use_skeleton = sk != nullptr && sk->use_2d == array_is_2d && (mi->surfaces[i].format_cache & RS::ARRAY_FORMAT_BONES);
			bool use_8_weights = mi->surfaces[i].format_cache & RS::ARRAY_FLAG_USE_8_BONE_WEIGHTS;
			
			if (mi->mesh->blend_shape_count) {
				SkeletonShaderGLES3::ShaderVariant variant = SkeletonShaderGLES3::MODE_BASE_PASS;
				uint64_t specialization = 0;
				specialization |= array_is_2d ? SkeletonShaderGLES3::MODE_2D : 0;
				specialization |= SkeletonShaderGLES3::USE_BLEND_SHAPES;