Is this the only time they can file indictments? If not, they may have additional charges in the works. I imagine they would have told the judge "this is all we're planning to file" if they didn't have any other investigative work going on, right?
[0] https://www.justice.gov/usao/justice-101/steps-federal-crimi...
No, a superceding indictment can be filed to add, remove, or update charges. The page you linked to has a good general introduction to the process, but you are mistaken to conclude from it that once an indictment is filed it cannot be altered, and that a separate parallel track would need to be opened up for new charges.
They can file more charges.