"I am not I; thou art not he or she; they are not they."
First of all, it’s not an epigraph – it’s the author’s note. But we figured this is as good a place as any to talk about it and, besides, it functions a bit like an epigraph; it’s just that the quote is from the author himself, not from another source. (Think of it as an egotistical epigraph.)
So what’s up with the author’s note? This here theory seems to be your best bet: Scholar Jane Mulvagh believes that the author’s note is Waugh’s little way of saying that Brideshead and the Flyte family are not fictional – they are based on a real family and a real estate – Madresfield. (Read all about it here.) If you buy it, then "I am not I; thou art not he or she; they are not they" is the author’s way of saying that Charles isn’t just Charles, Sebastian isn’t just Sebastian, etc. His novel is a mingling of the fictional and the real.