I find the Reference horns differ somewhat as regards intonation. Proper set-up is key, key height, etc. But I found recently that Selmer Necks are really inconsistant. I believe they have the biggest bearing with regards intonation, and even sound for that matter. One 54 neck I played recently was really bad and the intonation was all over the place. I placed my 54 neck on the that 54 and the intonation was significantly better, almost perfect.
The 54 is an awesome horn, provided it has a good neck. Selmer really needs to do a better job with their quality control. Just my opinion and experience.