Basically how I understand it. Marty is still Marty. He never affected his timeline. But since Marty altered Docs timeline two times. He didn't travel with Marty, in the second half. Doc still does his original mission: to get detailed history for Marty, and gets caught by Edna. But he goes back and forth to deal with his "home" life. Rather than running through time. Since he patched up his relationship, with his father. He just didn't know where Marty was, in time. So Marty had to leave him that clue. If Marty never fixed his relationship with his dad. Alternate Doc would of reverted back to real doc. At the end of Episode 2. But would of been really killed, by being run over.
I assume in this timeline. Marty used the Delorean alone, to fix Aurthur's Timeline. Since Doc was busy with the Key to the city. It's similar to the issue with Doc not remembering he dressed up Marty in that bad get up. Time didn't catch up to his memory.