The OEMs' justification for this is to try to make it harder for greybox importers/resellers or box shifters to tamper with the firmware on phones.
It's not unheard of for modified firmwares with malware to get put onto phones that are being sold into different markets.
If you need to register phones one by one, it slows the process down and makes it harder to modify a large number of phones, as they can try detect and prevent bulk requests. In theory that is believed to make it less likely that a customer buys their phone and ends up with a bad experience (keylogger in the modified firmware) that they attribute to the OEM.
There's obviously a self interest from OEMs to use this to also enforce market segmentation - they don't want people box shifting handsets from low margin markets into high margin markets and undercutting the official retail price. Some OEMs like Samsung have added region locks to their phones in the past because of this (which are released after 5 minutes of a call is made while connected to a mobile network from the original sales market.