Did you even read MT's measurement guide? There is no argument:
Measure your best fitting shirt. "RECOMMENDED"
Body measurement method: Many customers get this wrong the first time
If that doesn't make it clear that they prefer the shirt measurement over the body measurement, well, you must be pretty damned dense.
Now, to provide a "fix" to the problem...
Modern Tailor should automatically create a profile with the shirt measurements from your test shirt. This would allow you to have finer control over the details of your shirt without having to remeasure the whole thing yourself. Problem solved.