So, recently I've seen an uptick in stuff like SystemJS and Webpack on the clientside.
This basically kills userscripting, which is very rude.
However, you can still get around this by completely proxying everything.
Let's take pony.town for example. A very antiuserscripting site.
What you'll want to do is download the script used to bootstrap and edit it to your hearts desire. You can do this by popping open the inspector, and looking for the path needed. I have an old script that you can adapt if you so desire. Instead of having to access and overwrite things from window, without the contexts needed and being unable to peek inside closures, you can now just serve up your own modifications to the script.