Molded buttons on Kluson shafts have been part of PRS history for a long time and have been on/off/on the McCarty and many Singlecut models since 1994.
For me it isn't aesthetic issues, I just like using the Phase III tuning machines more. It's a stellar tuning machine for lots of reasons, but the practical one is that string changes are faster and simpler. I hate changing strings, and anything making that chore go a little faster I'm good with.
I realize that Paul says the Klusons give the guitars a better or more vintage tone by making the headstock lighter, or offering more string contact.
If offered the choice, however, I'd still want the Phase IIIs. Since I'm not offered the choice on some of the new models, I wouldn't bother changing them out, but I might piss and moan when changing strings!
Fortunately, my current PRS models have the Phase IIIs. So I'm content. For now.