HI Zack, it turns out that has many issues with things looking not the same for Mac/Linux/Windows, and this has been discussed and brought up in this list. But not all has been taken care yet. For Mac, the new Pd, so far, was changing things one way or another, and the way things changes in 0.48-test5 is not as bad as the first test releases :)
One of the issues is that Pd didn't have the same font for all systems, now it does (it's "Deja Vu"). There were also other changes, a new Tcl/Tk update (if I'm not mistaken) and a new way of rendering the fonts for retina on the Mac.
The issue you brought up with the documentation may happen not only for Cyclone, but any documentation that was designed in Pd Extended, or even for Purr Data. So one way to sort this out is adopting Pd Extended's font metrics. Dan says he could get a new branch running just to test this.
cheers