Most of us will say that machine built wheels generally do not have the evenness of spoke tension to do well. I've bought 3 sets of machine builts over the years where time or the resale price of the bike they were to go onto did not justify me doing builds. In all cases the wheels needed a tune up right out of the box to even up the tension. Add more tension after that and finally re-true.

So there may be a good middle ground for you in the option of getting a machine built wheel and then having a good wheel guy do a tune up on it before you even mount your first tire.

Frankly I think these two guys are trying to sell you a high profit margin handbuilt wheel. It's apparent that when they are replacing the spoke that they are ONLY replacing the spoke and not checking out the wheel to fix you up and ensure that this doesn't happen again. You're not getting any decent service from them. Especially if you bought the bike there. When the first spoke needed replacing it would be a very neglectful mechanic that didn't look the wheel over and tighten up any loose spokes or at least say "Come look at this. We can do a tune up to make sure you don't have any more troubles for $X." The fact that they didn't suggests that they aren't taking very good care of your new bike.