As someone who is at the tail end of opening a commercial space.  You are exactly right.  The best advice I can give is to find an architect that has designed similar space before, follow his plans to the 'T', and you will have very little difficulty.

Where I ran into problems is when the contractor thought it was o.k. to veer away from the plans.  The city inspectors made me change it all back.  Quite a costly mistake.  Not only in money, but in time.  Also, the architect did not understand my project, and the other mistake was using a contractor who was a relative.  Somehow, I managed to pull through despite all of that.

thats a tough one. We actually designed our space ourselves but gave those drawings to an architect who "doctored" them up correctly for the city. The city our place is in Southgate is pretty strict and wanted to see a full set of plans.

We decided against using any family for the project just in case and the contractor that has been doing the work has been great, sure some minor issues, but hey were building out a large space what do you expect. Its just like a house, you'll have changes, things wont be perfect, but you just gotta go with it and get it done.