### 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)

glGenBuffers(1, &s->blend_shapes[i].vertex_buffer);
				glBindBuffer(GL_ARRAY_BUFFER, s->blend_shapes[i].vertex_buffer);
				GLES3::Utilities::get_singleton()->buffer_allocate_data(GL_ARRAY_BUFFER, s->blend_shapes[i].vertex_buffer, size, p_surface.blend_shape_data.ptr() + i * size, (s->format & RS::ARRAY_FLAG_USE_DYNAMIC_UPDATE) ? GL_DYNAMIC_DRAW : GL_STATIC_DRAW, "Mesh blend shape buffer");
				if ((p_surface.format & (1 << RS::ARRAY_VERTEX))) {
					glEnableVertexAttribArray(RS::ARRAY_VERTEX + 3);
					glVertexAttribPointer(RS::ARRAY_VERTEX + 3, vertex_size, GL_FLOAT, GL_FALSE, stride, CAST_INT_TO_UCHAR_PTR(0));
				}
				if ((p_surface.format & (1 << RS::ARRAY_NORMAL))) {
					glEnableVertexAttribArray(RS::ARRAY_NORMAL + 3);
					glVertexAttribPointer(RS::ARRAY_NORMAL + 3, 2, GL_UNSIGNED_SHORT, GL_TRUE, stride, CAST_INT_TO_UCHAR_PTR(normal_offset));
				}
				if ((p_surface.format & (1 << RS::ARRAY_TANGENT))) {
					glEnableVertexAttribArray(RS::ARRAY_TANGENT + 3);
					glVertexAttribPointer(RS::ARRAY_TANGENT + 3, 2, GL_UNSIGNED_SHORT, GL_TRUE, stride, CAST_INT_TO_UCHAR_PTR(tangent_offset));
				}
			}
			glBindVertexArray(0);
			glBindBuffer(GL_ARRAY_BUFFER, 0);
		}
		
		glGenVertexArrays(1, &s->skeleton_vertex_array);
		glBindVertexArray(s->skeleton_vertex_array);
		glBindBuffer(GL_ARRAY_BUFFER, s->vertex_buffer);
		if ((p_surface.format & (1 << RS::ARRAY_VERTEX))) {
			glEnableVertexAttribArray(RS::ARRAY_VERTEX);
			glVertexAttribPointer(RS::ARRAY_VERTEX, vertex_size, GL_FLOAT, GL_FALSE, stride, CAST_INT_TO_UCHAR_PTR(0));
		}
		if ((p_surface.format & (1 << RS::ARRAY_NORMAL))) {
			glEnableVertexAttribArray(RS::ARRAY_NORMAL);
			glVertexAttribPointer(RS::ARRAY_NORMAL, 2, GL_UNSIGNED_SHORT, GL_TRUE, stride, CAST_INT_TO_UCHAR_PTR(normal_offset));