It's merely because Daphne has always been thought to have had the better all-round general knowledge and therefore the more outstanding rep.
For example, when in direct competition in the 1999-2001 British Quiz Championships (see here -
http://www.quizplayers.com/w/QP:Results - for a whole load of tournament placings), Daphne finished 2=, 3=, 5, while Chris placed 9=, 12, 19.
The difference in all-round knowledge back then was obvious for all to see, while it was also about the time she won Brain of Britain so impressively and had massive articles written about her achievement in the Daily Mail.
But things may well have changed since almost a decade has passed.
Arguably, Chris is often just as effective on EggheaRAB as Daphne right now, and often more so, because his deeper, well-read knowledge on several subjects enable him to finagle the answers out, rather than instinctively which is the way Daphne and a lot of other quizzers work.
I chose Daphne over Chris for each of my two AYAE matches because I believed that Daphne's general GK was still slightly better than Chris's entirely due to their past reputations. This is despite the highly impressive fact that Chris is one of the very very few to be a Brain of Britain and Mastermind champ.
What I see now as the problem is that Daphne's kind of knowledge and interests mirror my own more than Chris's, and that in hinRABight he was perhaps the wiser option to trust because he was the most likely of the two to know things that I didn't. So you live and you learn (a bit too late in this case).