I have Peruvian on my CU24 30th Anniversary PS, and had it on my first PRS acoustic, and Artist V. I love the tone on the CU24, and equally loved the tones on the other two I unfortunately no longer have. It's a beautifully resonant wood, IMHO. In fact, this wood really opened my eyes to the importance of neck wood tones.
So did the sinker mahogany on my Signature Limited; the guitar had a great tone, but of course with the very different pickups it's difficult to make a direct comparison.
I don't know what kind of mahogany is on the neck of the 20th PS Anni guitar, or my WL McCarty, but they both also sound great. I also don't know much about the type of mahogany that was on other PRSes I've owned over the years; I didn't think to ask.
All of my current electrics have an African ribbon mahogany back. I don't know what that does vs other types of mahogany, to be honest, but it sure looks beautiful and feels lighter than other types of mahogany I've had on other PRS guitars. And I'm truly happy with the tone of the instruments. They're certainly at the very least the equal of other mahogany types, if not an improvement -- but it's hard to know what causes what on this stuff.
Fretboards: I have three with Madagascar rosewood fretboards, and one with Brazilian. The Madagascar came on all three of my PS electrics, and the guitars sound gorgeous. My WL McCarty has the Brazilian, and it's perhaps got a little more snap or twang, but that might have nothing whatsoever to do with the type of fretboard.
Of the ones I have, I'll have to say that my most beautiful sounding guitar is the 20th PS Anniversary Limited model. It's got a bit thicker mahogany back; I have no idea what kind of mahogany neck; and the Madagascar fretboard. But...it also has the Paul's pickups and the Narrowfield middle pickup, and they're different from the others, so...apples to oranges, maybe. Honestly, they all sound amazing.
I'm not sure I have much of a point to make, except that I'm confident that whatever you choose, you're going to wind up a very happy camper. It's hard to screw this up, they are amazing at what they do.