I did some research and uncovered quite a debate on wether or not a set of stairs or deck should be flush with the exterior door threshold. Recently I was asked to replace some subfloor that had rotted through the floor of my family's mudroom. The front door to the mudroom had a set of stairs where the to step was flush with the threshold and the rear door had a deck that was placed 5" below the door opening. Both doors were only secured thorough the brick mold exterior trim. They had not been shutting well for a few years.
To fix the situation I replace both doors and flashed them with door wrap and ice and water shield
I installed a new deck mounted below the threshold 7.5" which is a standard rise.
I removed the rotted subfloor from beneath the doors and replaced and installed a new substrate and linoleum.
I guess I fall into the camp of mounting stairs and decks below the threshold to prevent driving rain , snow , and ice from easily entering your home and wreaking havoc!