Mainly because some people handload ammo for more than one rifle in the same chambering. Sometimes the chambers will be close enough in dimensions to handle neck-sized brass, but more often not. As an example, my wife and I own several rifles in .223 Remington. All shoot the same basic load well, but for the "same" load to work in all the rifles the cases need to be FL sized.
Plus, even if the same cases are always fired in the same rifle, after a few firings they often need FL sizing to chamber easily.
I segregate the brass for those situations where I have more than rifle in the same calibre. I haven't FL sized any rifle cases for years. I haven't had the need to do so. Maybe the day will come, but it hasn't yet, and some of those batches of brass have gone past 30 loading cycles.
The cases come out of the rifle smaller than the chamber, so unless a loose chamber has seen them bulged on one side (something you can avoid in future, if you know about it, by a bit of attention to the first fireforming) if they won't fit back in easily after reloading it is something that is being done to them in the reloading process.
FWIW I use several different brands of brass, and both rimmed and rimless (no belted), in a range of action types.
