The US Federal Government is the superior sovereign. Sovereign immunity is powerful but also specific in dealing with civil lawsuits, hence this very ruling. It doesn't apply to federal agency actions for example. It also in no way prevents Congress from carving out whatever exceptions it wants, in fact that's how civil lawsuits against the government in general happen, Congress passes laws saying "people may sue the government for this."

It'll actually be most interesting to see how this might ultimately affect other entities that have been using it, such as State Universities. This ruling didn't specifically address that, as usual courts like to stay specific to the case. But in their final paragraph CAFC clearly acknowledged the parallels with other cases, and it's hard to see how the same logic of this ruling wouldn't apply to any other such entity too.