I always considered it part of the tuning process. Each bow/arrow combo ultimately has that "sweet spot", where all the stars and planets align.
Once I'm almost to that point, I will play around with CF in or out (or up - gotta love tunable nocks) till I'm happy with one or the other.
I usually end up with CF out.
However, my favorite go-to bow, a Dale Dye TE, happens to have a preference for CF in. I get distinct fletching rub on the very edge of the shelf when shooting CF out. While this rubbing never seemed to have a negative impact on arrow flight, it had a negative affect on my mind....I knew it was happening! A bit of testing with CF in and powder...no more rub.
Hard to say that one way or the other is correct....many folks just shoot that way because someone told them to or "that's how I've always done it!". I seen a lot of BW shooters shoot CF up, because someone at BW recommended that way. Many of us "ol timers" probably shoot CF out by default, because that was the way we were taught.
Bottom line....don't shoot one way or the other because someone tells you to.....experiment on your own. We aren't talking some drastic change here. Ya never know.....one little change like that may make the stars and planets align!