So short answer, yes, holding After Hours tickets doesn't impact your park hopper ticket; you can do whatever you want with your day, aside from the "2 pm" rule.
Longer answer, for the benefit of others too: One of the things that confused me about After Hours tickets is that they are their own, well, ticket. You don't have to even have any other kind of park ticket that day. You could just show up to your AH park at 7pm at the end of, say, a hotel day in which you didn't go anywhere before that.