You've gotten specific advice from a structural engineer. W/O anyone here being able to see what you have, what is your concern? Have you expressed them to the engineer? If so, what did he/she say???
I guess if you live in an earthquake zone or in hurricane alley, why can't you go w/what the engineer says? Are you planning on having it inspected by either the engineer or municipal inspector? If you're REALLY worried, have them sign off on the design as YOU see fit.
Other than that, I don't know what to say. My best to ya and hope this helps.