### 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)

glDisable(GL_SCISSOR_TEST);
	glClearColor(0.0, 0.0, 0.0, 0.0);
	glClear(GL_COLOR_BUFFER_BIT);
	CanvasOcclusionShaderGLES3::ShaderVariant variant = CanvasOcclusionShaderGLES3::MODE_SDF;
	bool success = shadow_render.shader.version_bind_shader(shadow_render.shader_version, variant);
	if (!success) {
		return;
	}
	shadow_render.shader.version_set_uniform(CanvasOcclusionShaderGLES3::PROJECTION, Projection(), shadow_render.shader_version, variant);
	shadow_render.shader.version_set_uniform(CanvasOcclusionShaderGLES3::DIRECTION, 0.0, 0.0, shadow_render.shader_version, variant);
	shadow_render.shader.version_set_uniform(CanvasOcclusionShaderGLES3::Z_FAR, 0.0, shadow_render.shader_version, variant);
	LightOccluderInstance *instance = p_occluders;
	while (instance) {
		OccluderPolygon *oc = occluder_polygon_owner.get_or_null(instance->occluder);
		if (!oc || oc->sdf_vertex_array == 0) {
			instance = instance->next;
			continue;
		}
		Transform2D modelview = to_clip * instance->xform_cache;
		shadow_render.shader.version_set_uniform(CanvasOcclusionShaderGLES3::MODELVIEW1, modelview.columns[0][0], modelview.columns[1][0], 0, modelview.columns[2][0], shadow_render.shader_version, variant);
		shadow_render.shader.version_set_uniform(CanvasOcclusionShaderGLES3::MODELVIEW2, modelview.columns[0][1], modelview.columns[1][1], 0, modelview.columns[2][1], shadow_render.shader_version, variant);
		glBindVertexArray(oc->sdf_vertex_array);
		glDrawElements(oc->sdf_is_lines ? GL_LINES : GL_TRIANGLES, oc->sdf_index_count, GL_UNSIGNED_INT, 0);
		instance = instance->next;
	}
	texture_storage->render_target_sdf_process(p_render_target); 
	glBindVertexArray(0);
	glBindFramebuffer(GL_FRAMEBUFFER, 0);
}
RID RasterizerCanvasGLES3::occluder_polygon_create() {