Project setting added via GUI is removed when reset to default

### Tested versions

Found as far back as 4.1.1 - couldn't test any earlier version (editor froze when opening any dropdown menu, old Wayland problems maybe, doesnt matter)

### System information

Godot v4.3.dev5 - EndeavourOS SMP PREEMPT_DYNAMIC Fri, 08 Mar 2024 01:59:01 +0000 - Wayland - Vulkan (Forward+) - integrated AMD Radeon Graphics (RADV RENOIR) () - AMD Ryzen 7 5825U with Radeon Graphics (16 Threads)

### Issue description

Project settings created manually within the settings menu will be removed when reset to their default value

### Steps to reproduce

When creating a custom project setting (using the project settings dialogue), it will show up as not being at its default value (which is weird because it actually is, in theory) - see image 1.


Then, resetting it to the default will cause it to be deleted from the project settings, with the editor printing a few copies of the same warning:
`core/config/project_settings.cpp:352 - Property not found: x/y`
where `x/y` is whatever path was chosen for the setting:


However, it will still show up in the settings GUI until it is closed and reopened:


### Minimal reproduction project (MRP)

Basically impossible to have an MRP, as the whole bug is something being unexplicably deleted. A completely empty project suffices.

Start with core/config/project_settings.cpp around line 352 and reproduce the behavior from the Project Settings dialog in an empty project. Check why resetting a manually created setting removes it and leaves the open dialog stale; done means the setting remains available after reset without the Property not found warning.

Written by the indexing model from the issue text.