### 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)

ERR_FAIL_COND(multimesh->mesh.is_null());
	AABB aabb;
	AABB mesh_aabb = mesh_get_aabb(multimesh->mesh);
	for (int i = 0; i < p_instances; i++) {
		const float *data = p_data + multimesh->stride_cache * i;
		Transform3D t;
		if (multimesh->xform_format == RS::MULTIMESH_TRANSFORM_3D) {
			t.basis.rows[0][0] = data[0];
			t.basis.rows[0][1] = data[1];
			t.basis.rows[0][2] = data[2];
			t.origin.x = data[3];
			t.basis.rows[1][0] = data[4];
			t.basis.rows[1][1] = data[5];
			t.basis.rows[1][2] = data[6];
			t.origin.y = data[7];
			t.basis.rows[2][0] = data[8];
			t.basis.rows[2][1] = data[9];
			t.basis.rows[2][2] = data[10];
			t.origin.z = data[11];
		} else {
			t.basis.rows[0][0] = data[0];
			t.basis.rows[0][1] = data[1];
			t.origin.x = data[3];
			t.basis.rows[1][0] = data[4];
			t.basis.rows[1][1] = data[5];
			t.origin.y = data[7];
		}
		if (i == 0) {
			aabb = t.xform(mesh_aabb);
		} else {