Thanks James.
I’ve found it does make a difference, they need to be aligned on both axis. I have an Agfa Optima 1535 (a very cool little camera!), that the RF was off vertically. I was told by many on-line experts that it didn’t matter as long as it lined up horizontally. Yeah – no. The shots were back focusing but once I figured that out and compensated for it (easy to do) it now nails it. The shop that serviced it in LA for some reason couldn’t align it right, and my next LA option wanted Leica CLA money to do just that. So I passed and just compensate.
On topic – yours could have been knocked out when it was shipped to you, or just because it is a hard used prototype. I’ve seen your sample shots in other reviews so I know you know how to focus a camera!

In this prototype the rangefinder patch was definitely misaligned vertically. The images never matched, with one sitting just high of the other. It’s possible therefore that the rangefinder was also mis-calibrated horizontally, which would make focusing difficult. I’ve reached out for clarification and will update.