As others have said, if there is any tweaking you want to do or clearing needed, having it in the carboy gives you the opportunity to do so. However if you're done messing with it and it's just aging, the bottle is probably a better place for it in my opinion. The surface area of wine to O2 exposure is different in bottles and carboys, and the O2 transfer through the cork is a lot different than whatever you're using on the carboy. It's certainly a nuance, but not a trivial one. And there's no absolute rule... 2 respected experts in home wine making do completely different things. If I remember correctly, Tim Vandergrift bottles as soon as appropriate, while Danial Pambianchi has carboys of wine a decade old.