### 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)

glBufferData(GL_ARRAY_BUFFER, lc * 6 * sizeof(float), geometry.ptr(), GL_STATIC_DRAW);
			glBindBuffer(GL_ELEMENT_ARRAY_BUFFER, oc->index_buffer);
			glBufferData(GL_ELEMENT_ARRAY_BUFFER, 3 * lc * sizeof(uint16_t), indices.ptr(), GL_STATIC_DRAW);
			glBindBuffer(GL_ARRAY_BUFFER, 0);
			glBindBuffer(GL_ELEMENT_ARRAY_BUFFER, 0);
		}
	}
	
	Vector<int> sdf_indices;
	if (p_points.size()) {
		if (p_closed) {
			sdf_indices = Geometry2D::triangulate_polygon(p_points);
			oc->sdf_is_lines = false;
		} else {
			int max = p_points.size();
			sdf_indices.resize(max * 2);
			int *iw = sdf_indices.ptrw();
			for (int i = 0; i < max; i++) {
				iw[i * 2 + 0] = i;
				iw[i * 2 + 1] = (i + 1) % max;
			}
			oc->sdf_is_lines = true;
		}
	}
	if (oc->sdf_index_count != sdf_indices.size() && oc->sdf_point_count != p_points.size() && oc->sdf_vertex_array != 0) {
		glDeleteVertexArrays(1, &oc->sdf_vertex_array);
		GLES3::Utilities::get_singleton()->buffer_free_data(oc->sdf_vertex_buffer);
		GLES3::Utilities::get_singleton()->buffer_free_data(oc->sdf_index_buffer);
		oc->sdf_vertex_array = 0;
		oc->sdf_vertex_buffer = 0;