I have made changes, cosmetic only, to exactly one PRS guitar (heck, one guitar ever, IIRC): my 2014 SE Zach Myers Spalted Maple top that looked really good in black pup rings and switch tip, and with pup covers.
Everything else (other than a couple TRC swaps, one to return to the correct stock TRC) is as I got it. And that is pure stock, AFAIK, except in one singular case: my Core Santana signature has EVH Wolfgang pickups (and sounds really good, btw) installed by a previous owner. There may be changes made to pre-owned guitars I have, but I'm not aware of them and otherwise assume they are stock.
About 1/3 of my guitars were acquired bland new - the rest are pre-owned acquisitions.
I don't swap pickups. I don't replace electronics, except when they fail (I did put a new pup selector switch in a Godin Freeway).
I don't know why, but I'd rather use the guitar as-created and explore what makes it different vs swapping out pups to make it sound just like every other guitar I have.
Maybe I just don't trust my own soldering skills and I'm too cheap to take it to someone else to modify.
Oh, I just remembered one other guitar I had modified - my Norman acoustic came without any kind of pickup, so I had a piezo pickup installed under the bridge.
And now that my memory is working, I installed a pickup in a mandolin myself (K&K type, drilled out the end pin), and added an adhesive-type pickup to a mandola (which works remarkably well).