### 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)

case RS::ARRAY_COLOR: {
						attrib_stride += sizeof(uint32_t);
					} break;
					case RS::ARRAY_TEX_UV: {
						attrib_stride += sizeof(float) * 2;
					} break;
					case RS::ARRAY_TEX_UV2: {
						attrib_stride += sizeof(float) * 2;
					} break;
					case RS::ARRAY_CUSTOM0:
					case RS::ARRAY_CUSTOM1:
					case RS::ARRAY_CUSTOM2:
					case RS::ARRAY_CUSTOM3: {
						int idx = i - RS::ARRAY_CUSTOM0;
						uint32_t fmt_shift[RS::ARRAY_CUSTOM_COUNT] = { RS::ARRAY_FORMAT_CUSTOM0_SHIFT, RS::ARRAY_FORMAT_CUSTOM1_SHIFT, RS::ARRAY_FORMAT_CUSTOM2_SHIFT, RS::ARRAY_FORMAT_CUSTOM3_SHIFT };
						uint32_t fmt = (p_surface.format >> fmt_shift[idx]) & RS::ARRAY_FORMAT_CUSTOM_MASK;
						uint32_t fmtsize[RS::ARRAY_CUSTOM_MAX] = { 4, 4, 4, 8, 4, 8, 12, 16 };
						attrib_stride += fmtsize[fmt];
					} break;
					case RS::ARRAY_WEIGHTS:
					case RS::ARRAY_BONES: {
						
						bool use_8 = p_surface.format & RS::ARRAY_FLAG_USE_8_BONE_WEIGHTS;
						skin_stride += sizeof(int16_t) * (use_8 ? 16 : 8);
					} break;
				}
			}
		}
		int expected_size = stride * p_surface.vertex_count;
		ERR_FAIL_COND_MSG(expected_size != p_surface.vertex_data.size(), "Size of vertex data provided (" + itos(p_surface.vertex_data.size()) + ") does not match expected (" + itos(expected_size) + ")");