It's really just a technicality thing, it has to do with the list of phones Apple sells that come from the factory that are not in a carrier locked state, essentially, the difference is the carrier locked phones are issued to that carrier and locked to their SIM (or IMEI number really). When it is removed, the phones (as far as function goes) are identical, but there is still a chance that the phone retains some pieces that identify it as a once carrier locked phone (and some people have reported that at times, the post purchase unlocked phones can revert back to being carrier locked for whatever reason...reset, restore, etc etc etc).
One of the major difference is if you ever have warranty work done (where a replacement is required), make sure Apple knows your phone is unlocked before they take it back (if you've done an IMEI unlock online or something), otherwise they'll replace your phone with another carrier LOCKED version and you'll have to go through the process again (and pay again)...this happened to my friend who used the eBay method many of us used when the iPhone 5 came out, he had Apple Care + and he dropped his and had it replaced, but when he got the new one, it was simply an AT&T carrier locked version (since that is what he initially bought), he had to drop a few bucks again to have it unlocked (which isn't a huge deal but might be for somebody).
There was also the major difference between software unlocked phones vs. factory unlocked phones...but that has to do with jailbreaking and what not (which is a whole other story and not really applicable here). In that case, there is a MASSIVE difference between the two, but that discussion is for another time.
In the end, there's no big difference, it's mainly just in the background details is all, and shouldn't affect functionality.