I think a lot will depend on what your wife's fit issues are. There are smaller frames, and they are often done with women/girls, and adolescent boys in mine. In theory, compared to a male of the same height, a female will have longer legs and a shorter torso. So smaller frames often have shorter top tubes. Of course most of us are not text book with our fit needs. I have short legs and a long torso, and have one custom bike, but I almost always can find a stock frame that fits me.
Georgina Terry had a bike company that sold women's bikes with a 700c rear wheel and a smaller front wheel. Georgina sold her company and retired, but she still dabbles. Last I heard she was equipping stock frames made by Waterford. I think she is in New York. Her bikes are not cheap but they are not outrageous either. It worth your time to visit her web site.
So if you are not interested on Georgina Terry then I think your next stop is to find a bike shop that you trust and work with them. Just remember that fitting a race bike is nothing like fitting a touring bike. I guess it also goes without saying that if they steer you to go custom, that a bike company known for custom racing bikes, may know squat about doing a custom touring bike.
I think I would avoid a custom touring bike for your first touring bike. Unless you are rich and money is no object, or a very confident that touring is something that you want to do, I would start with something more off the shelf.
Why are you insisting on a thru axle? This will limit your choices and it is not required for most touring.
