MultiMesh3D throws errors and can corrupt scenes, Condition "instance_count > 0" is true.

### Tested versions

4.2.1 bot standard and mono

### System information

Windows 11 - Vulkan - Nvidia RTX 4070 - intel i5 13600KF

### Issue description

For some reason MultiMesh3D now throws an error like this:

(screenshot is from mono version but same error happens in the standard godot version)

and it can also lead to scene corruption - I don't know the conditions for that, sometimes my scenes just get corrupted when I add the multimesh, I have no idea why, it's not any particular mesh itself I tried built-in ones too.

### Steps to reproduce

With MRP:
Open the project if you don't see the error on the first try (no .godot folder yet so it doesn't show) then close the project and open it again, you should see it now or after opening the scene with the MultiMesh3D (called planet.tscn) - you might need to have both scenes open when you close the project so they reopen.
(sometimes under no idea what circumstances you can get a corrupted scene error and the scene will no longer open though I have no idea why or how to reproduce this)

Without MRP:
1. Make a scene with MultiMesh3D and populate a surface with some MeshInstance3D (for testing I used the Cylinder mesh) and save it as a scene.
2. Instantiate that scene into your main scene.
3. Run your project.
4. Close the project and open it again
5. You should see the error now or after opening the scene with the MultiMesh3D.

### Minimal reproduction project (MRP)

[MultiMeshMRP.zip](https://github.com/godotengine/godot/files/13930789/MultiMeshMRP.zip)

Start with the attached MultiMeshMRP.zip and follow the listed steps for MultiMesh3D, including closing and reopening the project and opening planet.tscn. Compare the error and any scene corruption across the standard and mono versions; done means the reported condition no longer appears and the scene remains openable after restarting.

Written by the indexing model from the issue text.