This is my understanding, having spoken with a few ADs. I have also noticed the 39mm models to have reduced availability the past few months. I have the 39mm chrono with white (non contrast) dial, and I prefer both its size, proportions, dial layout and presence to the 41mm, which I consider to be less differentiated from the offshores. The 41mm is still a beautiful watch of course, and all depends on what you believe will work better for you in the long term.
As a long-time Royal Oak fan, I was bit disappointed that AP decided to upsize virtually the entire line-up except for the new 15202. So I bought the new 15202, although that will be the subject of a different post with pics...
Good luck with your decision!