### 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)

specialization |= SkeletonShaderGLES3::USE_TANGENT;
					}
				}
				bool success = skeleton_shader.shader.version_bind_shader(skeleton_shader.shader_version, variant, specialization);
				if (!success) {
					continue;
				}
				Transform2D transform = mi->canvas_item_transform_2d.affine_inverse() * sk->base_transform_2d;
				skeleton_shader.shader.version_set_uniform(SkeletonShaderGLES3::SKELETON_TRANSFORM_X, transform[0], skeleton_shader.shader_version, variant, specialization);
				skeleton_shader.shader.version_set_uniform(SkeletonShaderGLES3::SKELETON_TRANSFORM_Y, transform[1], skeleton_shader.shader_version, variant, specialization);
				skeleton_shader.shader.version_set_uniform(SkeletonShaderGLES3::SKELETON_TRANSFORM_OFFSET, transform[2], skeleton_shader.shader_version, variant, specialization);
				Transform2D inverse_transform = transform.affine_inverse();
				skeleton_shader.shader.version_set_uniform(SkeletonShaderGLES3::INVERSE_TRANSFORM_X, inverse_transform[0], skeleton_shader.shader_version, variant, specialization);
				skeleton_shader.shader.version_set_uniform(SkeletonShaderGLES3::INVERSE_TRANSFORM_Y, inverse_transform[1], skeleton_shader.shader_version, variant, specialization);
				skeleton_shader.shader.version_set_uniform(SkeletonShaderGLES3::INVERSE_TRANSFORM_OFFSET, inverse_transform[2], skeleton_shader.shader_version, variant, specialization);
				glBindVertexArray(mi->mesh->surfaces[i]->skeleton_vertex_array);
				_compute_skeleton(mi, sk, i);
			}
		}
		mi->dirty = false;
		if (sk) {
			mi->skeleton_version = sk->version;
		}
		dirty_mesh_instance_arrays.remove(&mi->array_update_list);
	}
	glDisable(GL_RASTERIZER_DISCARD);
	glBindBuffer(GL_ARRAY_BUFFER, 0);
	glBindBufferBase(GL_TRANSFORM_FEEDBACK_BUFFER, 0, 0);
}
RID MeshStorage::multimesh_allocate() {