I just purchased a Surly Cross Check and while I have toe overlap, the bike feels so good and does everything I want. Toe overlap is not a big deal to me, but the 26" wheels on the Trucker were. I have two sets of wheels, one with 25mm tires and a touring set with big honkin' 38mm tires. Even with the 38mm tires there is room for fenders. Don't worry about wasting his time. You are going to drop some bucks, and that's what he does. Make sure it's what YOU want and if you love it, then he shouldn't mind making it have all that you want on it.
Claudia
2009 Trek 7.6fx
2013 Jamis Satellite
2014 Terry Burlington