Why does HTTP Switchboard mess with my settings?

It does not mess with your settings. That's unfortunate that this is being said sometimes, as it is without basis. It's is pure disinformation (I don't care whether it is willful or not, result is the same).

Your settings are always there after you install HTTP Switchboard ("HTTPSB"). Uninstall it, and they will take precedence.

In fact, they may even take precedence if HTTPSB is installed, since HTTPSB won't create rules which are more fine-grained than rules based on hostname.