Skip the numbers
If you like your current bike, I'd ask them to build something with similar geometry. If they're going to recommend a change, ask them why they think that's a good idea for YOU. Ask them if there's a way you can try one out with the geometry they're proposing.
It's amazing... we all spend so much time telling newbies and friends to go in and buy the bike that fits, since the component groups are usually the same across a given price point. But I've read so many posts in here about people having custom frames built, and they forget that same advice.
I build custom furniture for a living, and one of the things I tell my clients is that the joy of custom work is that you get to have something built the way you want it to be built, instead of simply choosing from whatever you're being offered by stores and catalogs. It's true that many people don't always know what they really want, and offering options helps... but if you're having them build a bike for you, and they're offering you an option, test that option out before you decide to have them integrate it.
As a custom shop, I'm assuming they know what they're doing, and they should be able to intelligently advise you if you have questions. And it's entirely possible that, after talking to you, they thought that this might be a good fit. But they should be able to explain the reasoning to you, AND be able to let you try it out to make sure. The money is yours, the bike will be yours when it's done, for better or worse, and NOW is your opportunity to have it built EXACTLY the way you want it to be. If you're happy with your current geometry, then I'd stick with it. If there's something you'd like to see done differently, then have your bike built that way. It's possible that the different angle is there to compensate for the geometry of their chosen fork, and the amount of trail will be the same, or maybe it's just something they feel like trying out. But if you want it to be built differently, tell them so.
It will be your bike, in a way that a hand-picked, professionally fitted factory bike won't be. It should therefore be built to accommodate your anatomical quirks and the way you really like to ride. There should be no complaints, because any deficiencies you feel your current ride has, should be able to be remedied in this new bike. It should be the best bike you've ever had, because it's specifically tailored to you, your desires, and your riding style... and THAT'S what makes it cool.
Custom shops have the privilege of getting to work in their chosen field, and I can say from experience that it's a joy to be able to work for yourself, doing what you enjoy doing. But you still have to work for the man with the money, and make sure that you give him what he wants. If I want a nice Cherry trestle table for my dining room, I can build one. But If you came in wanting something else, it would be wrong of me to try to force my vision for a pretty table on you. It's ok to make recommendations if the client isn't really sure what it is he/she wants, but in the end, it's their money, and they have to live (and pay for) with the results, so it's their decision.