Position of object in Remote tab during Run Project is not the same position as in-code

### Tested versions

-Reproducible in 4.3 stable, 4.4 beta1, and the current 4.4 rc1

### System information

Windows 10 - Godot v4.4-rc1 - Vulkan1.3.260 - Forward+ - AMD Radeon Graphics

### Issue description

When using the Remote tab during project play to inspect each object, I do not know why the objects - either the parent node or its children - are not in the position I know they should be in.

### Steps to reproduce

If you don't want to open the project I've attached, you can create a simple project with an object whose child node is a MeshInstance3D. Any mesh and material will do. You can also attach other child nodes either to the parent object or the MeshInstance3D, though it isn't necessary. Then instantiate that object in the main class you're running the project from. Finally, go to the Remote tab and click on each of the object's child nodes.

### Minimal reproduction project (MRP)

[test_2025-02-24_17-52-34.zip](https://github.com/user-attachments/files/18950978/test_2025-02-24_17-52-34.zip)

Open the attached minimal reproduction project and reproduce the discrepancy by running it, then inspecting the instantiated object and its children in the Remote tab. Read the editor's remote-scene inspection and transform-display path to determine where runtime positions diverge from the in-code view. Done means parent and child positions appear consistently in the Remote tab.

Written by the indexing model from the issue text.