Toe strikes can really suck with fenders. But the only way to really avoid overlap is to use small wheels (using shorter cranks and avoiding toe clips help, but nowhere near as much). For medium-to-large frame sizes, 26" is small enough. I haven't run the numbers on smaller frames. It seems that many people live with the annoyance, so even though I think overlap is something to avoid on a commuting rig if at all possible, I would not consider the shop grossly negligent for failing to discuss this with you.