Hi Huey,
Nice to see a local (to me) post a response - I live in Concord.
The overlap with just the tire isn't what bothers me... without a fender my foot just slides against the tire without causing much trouble. The fender is what gets me though, cause more of my foot catches, and its more likely to stick and cause me to low side.
I come from a MTB background, where this is pretty much never an issue. The only other road bike I had fenders on before this one was an old Raleigh, which had miles of room for whatever I wanted, so it never occurred to me to look into this before buying this bike. I guess since this never happened to me before now, I kinda freaked out when it did the first time. It happened again on the way home that same day, and I took the fenders off that night. I'm sure that you are right, a little practice around the neighborhood would probably help.
All the same though, is this common in modern road bikes, or did I get the lucky bike with a short front center? I can't be the only one with this issue...?