### 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)

Transform3D mtx;
					mtx.basis.rows[0][0] = dataptr[0];
					mtx.basis.rows[0][1] = dataptr[1];
					mtx.origin.x = dataptr[3];
					mtx.basis.rows[1][0] = dataptr[4];
					mtx.basis.rows[1][1] = dataptr[5];
					mtx.origin.y = dataptr[7];
					AABB baabb = mtx.xform(skbones[j]);
					if (first) {
						laabb = baabb;
						first = false;
					} else {
						laabb.merge_with(baabb);
					}
				}
			} else {
				for (int j = 0; j < bs; j++) {
					if (skbones[j].size == Vector3(-1, -1, -1)) {
						continue; 
					}
					const float *dataptr = baseptr + j * 12;
					Transform3D mtx;
					mtx.basis.rows[0][0] = dataptr[0];
					mtx.basis.rows[0][1] = dataptr[1];
					mtx.basis.rows[0][2] = dataptr[2];
					mtx.origin.x = dataptr[3];
					mtx.basis.rows[1][0] = dataptr[4];
					mtx.basis.rows[1][1] = dataptr[5];
					mtx.basis.rows[1][2] = dataptr[6];
					mtx.origin.y = dataptr[7];