A very basic example: if you had a large site, you can raise my Google Page Speed score by inlining all CSS and JS, but that would be stupid because it doesn't take into account the next page load and caching. I've seen some render blocking optimizations slow the overall page too. Getting rid of query strings is nice, but sometimes you need it for cache busting and other things, but it penalizes your score. Even Google's own tag manager/analytics scripts lowers your page speed score when they are on the site.