Missing required editor-specific import metadata for a texture ... when checking out a new project/plugin

[Maran23]

Tested versions

Godot 4.2
But the version doesn't matter.

System information

Godot v4.2.stable - Windows 10.0.19045 - Vulkan (Forward+) - dedicated AMD Radeon RX 6900 XT (Advanced Micro Devices, Inc.; 31.0.22023.1014) - AMD Ryzen 9 5900X 12-Core Processor (24 Threads)

Issue description

When you checkout a new project or plugin (e.g. via Git, AssetLib) that uses icons where the import setting were modified, an error is spamed in the log for every icon.

Example:

• icon.svg with import settings modified
• Missing required editor-specific import metadata for a texture (please reimport it using the 'Import' tab): 'res://.godot/imported/icon.svg-218a8f2b3041327d8a5756f3a245f83b.editor.meta'

Steps to reproduce

1. Modify an icon (e.g. the default icon.svg)
   
2. Change an import setting (e.g. Scale With Editor Scale)
   
3. Close Godot and delete the .godot folder (To simulate a new project, e.g. when someone is checking out the project it will not exist yet)
4. Open Godot, see that there will be an error printed to the console

Details:
When changing some setting the has_editor_variant flag is set. In this case Godot expects that there must be a file in the .godot folder, and prints an error when not.
Content of the icon.svg.import

Note:
The icons will work fine from my testing, e.g. Scale With Editor Scale works even though the error was printed. The import file is also created after the error was printed, so this is fine as well.

Minimal reproduction project (MRP)

Icon.zip

[Maran23]

Introduced by: #75949