### 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)

continue;
					}
					skeleton_shader.shader.version_set_uniform(SkeletonShaderGLES3::BLEND_WEIGHT, weight, skeleton_shader.shader_version, variant, specialization);
					skeleton_shader.shader.version_set_uniform(SkeletonShaderGLES3::BLEND_SHAPE_COUNT, float(mi->mesh->blend_shape_count), skeleton_shader.shader_version, variant, specialization);
					glBindVertexArray(mi->mesh->surfaces[i]->blend_shapes[bs].vertex_array);
					_blend_shape_bind_mesh_instance_buffer(mi, i);
					glBindBufferBase(GL_TRANSFORM_FEEDBACK_BUFFER, 0, mi->surfaces[i].vertex_buffers[1]);
					glBeginTransformFeedback(GL_POINTS);
					glDrawArrays(GL_POINTS, 0, mi->mesh->surfaces[i]->vertex_count);
					glEndTransformFeedback();
					SWAP(mi->surfaces[i].vertex_buffers[0], mi->surfaces[i].vertex_buffers[1]);
				}
				uint32_t bs = mi->mesh->blend_shape_count - 1;
				float weight = mi->blend_weights[bs];
				glBindVertexArray(mi->mesh->surfaces[i]->blend_shapes[bs].vertex_array);
				_blend_shape_bind_mesh_instance_buffer(mi, i);
				specialization |= can_use_skeleton ? SkeletonShaderGLES3::USE_SKELETON : 0;
				specialization |= (can_use_skeleton && use_8_weights) ? SkeletonShaderGLES3::USE_EIGHT_WEIGHTS : 0;
				specialization |= SkeletonShaderGLES3::FINAL_PASS;
				success = skeleton_shader.shader.version_bind_shader(skeleton_shader.shader_version, variant, specialization);
				if (!success) {
					continue;
				}
				skeleton_shader.shader.version_set_uniform(SkeletonShaderGLES3::BLEND_WEIGHT, weight, skeleton_shader.shader_version, variant, specialization);
				skeleton_shader.shader.version_set_uniform(SkeletonShaderGLES3::BLEND_SHAPE_COUNT, float(mi->mesh->blend_shape_count), skeleton_shader.shader_version, variant, specialization);
				if (can_use_skeleton) {
					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);