### 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)

l = l->next_ptr;
				continue;
			}
			CanvasLight *clight = canvas_light_owner.get_or_null(l->light_internal);
			if (!clight) { 
				l->render_index_cache = -1;
				l = l->next_ptr;
				ERR_CONTINUE(!clight);
			}
			Vector2 canvas_light_dir = l->xform_cache.columns[1].normalized();
			state.light_uniforms[index].position[0] = -canvas_light_dir.x;
			state.light_uniforms[index].position[1] = -canvas_light_dir.y;
			_update_transform_2d_to_mat2x4(clight->shadow.directional_xform, state.light_uniforms[index].shadow_matrix);
			state.light_uniforms[index].height = l->height; 
			for (int i = 0; i < 4; i++) {
				state.light_uniforms[index].shadow_color[i] = uint8_t(CLAMP(int32_t(l->shadow_color[i] * 255.0), 0, 255));
				state.light_uniforms[index].color[i] = l->color[i];
			}
			state.light_uniforms[index].color[3] *= l->energy; 
			if (state.shadow_fb != 0) {
				state.light_uniforms[index].shadow_pixel_size = (1.0 / state.shadow_texture_size) * (1.0 + l->shadow_smooth);
				state.light_uniforms[index].shadow_z_far_inv = 1.0 / clight->shadow.z_far;
				state.light_uniforms[index].shadow_y_ofs = clight->shadow.y_offset;
			} else {
				state.light_uniforms[index].shadow_pixel_size = 1.0;
				state.light_uniforms[index].shadow_z_far_inv = 1.0;
				state.light_uniforms[index].shadow_y_ofs = 0;
			}
			state.light_uniforms[index].flags = l->blend_mode << LIGHT_FLAGS_BLEND_SHIFT;
			state.light_uniforms[index].flags |= l->shadow_filter << LIGHT_FLAGS_FILTER_SHIFT;