I'm running the stock Super 3 and I love it, but I'm into that dark tone.
Great mid and low tones. The HS2 in the middle makes up for it as it's fairly brite.
Yes... I actually use the pickup selector on my guitars.

I have thought about trying an SD Custom Custom, but I don't feel like tearing into it.
I use a Custom Custom in my RG560 and it sounds great with the Basswood body, very articulate.
Not sure how it would sound with Mahogany.