### Godot version

4.1.1-stable

### System information

Windows 10

### Issue description

When the project loads in editor, all the settings defined in project settings will be loaded over the default values, but when running the game nearly 95% of them will be ignored resulting in just loading the default settings.

here it's just loading only 4 variables from project setting and i have added the fifth in this pull request https://github.com/godotengine/godot/pull/80151
![image](https://github.com/godotengine/godot/assets/53877170/926168a6-e6d3-4983-b59d-7fd202db681d)

}
		}
	}
	if (oc->line_point_count != lines.size() && oc->vertex_array != 0) {
		glDeleteVertexArrays(1, &oc->vertex_array);
		GLES3::Utilities::get_singleton()->buffer_free_data(oc->vertex_buffer);
		GLES3::Utilities::get_singleton()->buffer_free_data(oc->index_buffer);
		oc->vertex_array = 0;
		oc->vertex_buffer = 0;
		oc->index_buffer = 0;
	}
	if (lines.size()) {
		Vector<uint8_t> geometry;
		Vector<uint8_t> indices;
		int lc = lines.size();
		geometry.resize(lc * 6 * sizeof(float));
		indices.resize(lc * 3 * sizeof(uint16_t));
		{
			uint8_t *vw = geometry.ptrw();
			float *vwptr = reinterpret_cast<float *>(vw);
			uint8_t *iw = indices.ptrw();
			uint16_t *iwptr = (uint16_t *)iw;
			const Vector2 *lr = lines.ptr();
			const int POLY_HEIGHT = 16384;
			for (int i = 0; i < lc / 2; i++) {
				vwptr[i * 12 + 0] = lr[i * 2 + 0].x;
				vwptr[i * 12 + 1] = lr[i * 2 + 0].y;
				vwptr[i * 12 + 2] = POLY_HEIGHT;
				vwptr[i * 12 + 3] = lr[i * 2 + 1].x;
				vwptr[i * 12 + 4] = lr[i * 2 + 1].y;