The solution is simple. Continue calling the boat Boaty McBoatface. Ignore all references to the government's preferred name. They can choose what's painted on the side, but the name depends only on what people call it. If enough people call it Boaty McBoatface its name really is Boaty McBoatface. If your job depends on calling it the government's preferred name then subtly alter the timing of your speech to make it…
This is good advice. In Toronto we have a baseball stadium called the Rogers Center (https://en.wikipedia.org/wiki/Rogers_Centre). It was originally called the SkyDome but it was bought by a company called Rogers and renamed.
Everyone still refers to it as the Skydome. Corporate branding be damned:)