Do they break them in at the factory? Mine spent a week being broken in before they shipped them. It must make a difference or they wouldn't spend time doing it.
I think I'd ask the dealer and/or Magico if you haven't already.
I also wonder if the new speakers are more revealing than your old speakers. You've spent 20 years selecting gear and cables (I assume) that work with them.
I think you'll get great sound. Might take more break in and tweaking.
I'm also running subs. My speakers are rated pretty flat down to 28hz, but they don't move air like a sub will. I suspect your speakers are the same. From what I've read, they prioritize tight bass.