I reckon what will happen (which I kind of hope) is that you'll come across the surviving characters in your new persona. But it's likely to be less of a huge part of the story. If you told Clem to find Omid and Krista, there's a chance you'll meet them together, maybe team up with them in a chapter, but nothing too grand really. The options are pretty vast; if you told her to trust nobody, you may never see her again, or for a fleeting moment. Or you meet Omid and Krista elsewhere (not sure on all the options as I went first across the sign to the Marsh House so we were split up), but no Clem if she wasn't told where to meet up with them. Or just Clem, the options have been laid out. Same with location, be it if you planned to leave by train, boat, in the countryside.
I'm very interested in how TTG carry this on, but personally I wouldn't want to be Clem's keeper. Don't get me wrong, I cared more for Clem than some people in the real world, but Lee trained her to fend for herself, seems like a step back to then put her in someone else's hands all over again. Connecting her with someone else would weaken the relationship gained between her and Lee in my eyes