### 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)

glDeleteTextures(1, &state.shadow_texture);
			glDeleteRenderbuffers(1, &state.shadow_depth_buffer);
			state.shadow_fb = 0;
			state.shadow_texture = 0;
			state.shadow_depth_buffer = 0;
			WARN_PRINT("Could not create CanvasItem shadow atlas, status: " + GLES3::TextureStorage::get_singleton()->get_framebuffer_error(status));
		}
		GLES3::Utilities::get_singleton()->texture_allocated_data(state.shadow_texture, state.shadow_texture_size * data.max_lights_per_render * 2 * 4, "2D shadow atlas texture");
		glBindFramebuffer(GL_FRAMEBUFFER, GLES3::TextureStorage::system_fbo);
	}
}
void RasterizerCanvasGLES3::render_sdf(RID p_render_target, LightOccluderInstance *p_occluders) {
	GLES3::TextureStorage *texture_storage = GLES3::TextureStorage::get_singleton();
	GLuint fb = texture_storage->render_target_get_sdf_framebuffer(p_render_target);
	Rect2i rect = texture_storage->render_target_get_sdf_rect(p_render_target);
	Transform2D to_sdf;
	to_sdf.columns[0] *= rect.size.width;
	to_sdf.columns[1] *= rect.size.height;
	to_sdf.columns[2] = rect.position;
	Transform2D to_clip;
	to_clip.columns[0] *= 2.0;
	to_clip.columns[1] *= 2.0;
	to_clip.columns[2] = -Vector2(1.0, 1.0);
	to_clip = to_clip * to_sdf.affine_inverse();
	glBindFramebuffer(GL_FRAMEBUFFER, fb);
	glViewport(0, 0, rect.size.width, rect.size.height);
	glDepthMask(GL_FALSE);
	glDisable(GL_DEPTH_TEST);
	glDisable(GL_BLEND);
	glDisable(GL_CULL_FACE);