I think that the message you saw gives the explanation: links to the DiskManagement framework need to be in place before diskutil can run, and those links have not by default yet been established in SUM. Hence the need for AppleJack.
Now that you are up and running, as VK intimates, there is no point in running Repair Permissions other than in Disk Utility or Terminal, no advantage whatsoever. In fact, Repair Permissions is often advocated but rarely needed. It is not something that needs to be done as a routine. "Repair Permissions" is available in AppleJack primarily as something to try on those occasions when your Mac just refuses to boot normally.
I usually recommend that only AppleJack's items 1, 3 and 5 should be used without good reasons for 2 and 4. Even that can sometimes be overkill, even counter-productive - there is a fetish for clearing caches which usually only gives the user a slower Mac until certain caches have been rebuilt.
Anyway, I'm delighted that you seem to have solved your problem. 🙂