I had emailed yellowjersey.com, since they still show the older RD5000 on their website and apparently it works great. They told me:

"New version is called "RD2". Sugino changed over late in 2007"

and in follow-up regarding the chainline issue:

"Hasn't been a problem.
I think the change was in honesty and accuracy more than an actual chainline change."

I already knew about the change and had seeen the 45mm listed on Sugino's website. Regardless of what YJ said in the email, people here always indicate that the chainline in fact did change in real-life use, and the RD2 doesn't work as well. I wound up buying slightly used S75's.

Also - though YJ has the RD5000 on their site, apparently they don't have it in stock. They just haven't updated their website in a while.