I should have posted an update sooner, but upgrading to the latest nightly did not actually fix this problem. By upgrading to the nightly I was forced to run the installer again, and the installer accepted my new (.website) TLD. However, when I decided to migrate the site to https I went to the site config to change the URL accordingly. Like before, it complained that I was entering an invalid URL. My solution was to run the installer again and import the preexisting database.
It would seem useful to disable the URL checking completely. After all, what if someone wanted to run Geeklog on an internal network with local domains?