Mueller's jusrisdiction in that case was being challenged, and he needed a win there or else the bulk of his efforts would be exposed as a house of cards.
Rosenstein had testified before Congress that Mueller was well in control, "no fishing expeditions here," so shared the need to shore up the house of cards.
Absent a challenge in open court, neither Mueller nor Rosenstein had any need to clarify the scope of the fishing expedition. The letter makes it clear, anybody associated with the Trump campaign is fair game, for anything they did, ever. Identify the people, search for crimes.
>>I think Mueller’s request for clarity and the letter response from Rosenstein was driven mostly by events in the Manafort case.<<
I think it’s more likely that the clarification was needed to keep Mueller and Horowitz (and eventually Huber) from bumping heads.
The real collusion story obviously resides in the Democrat/Hillary circles and if Mueller followed his original charge, he would have ended up investigating the FBI and DOJ, Fusion GPS, Hillary’s campaign, etc. The new instructions probably served to limit the scope of his original charge, as indicated by the last part of Rosenstein’s letter where he says that anything outside of the scope of the investigations listed there must first be cleared with Rosenstein.