One solution to make the issue less likely to happen is to reduce the padding on the links with custom CSS.
Unfortunately there is no complete solution at this time. Longer usernames or more icons can always cause the design to break again...
At this time, the best course of action would be for FoF Links to handle it, by using a dropdown for its excess links. But fundamentally it's a Flarum issue because other extensions might also add stuff to that bar and there's no plan in place for when it inevitably becomes too long.
Fixing the alignment of left and right to keep them in the navigation wouldn't really solve the issue because then some controls would be above each other and become inaccessible.