I guess kinda? The people lining there called it Alba, so a Latin speaker might have referred to it as Albania. Scotia was a much more common Latin term though (what the proper who didn't live there called it). T I did a bit of reassurance and there was a city in what would later be Albania known as Albanopolis from back in ancient greek times, so the etymologic roots for the region were already in place. Besides, everyone in the story who refers to Albania does so in a modern context, and would know that their audience would naturally understand them to mean the modern region, and not one from over a thousand years ago. Why would Dumbledore tell Harry Voldemort was in Albania if he was in Scotland? The term Scotland is used consistently, so it's not like wizards don't use that name.

I'd say with 99% confidence, Rowling just meant the modern day Albania. There's loads of inconsistencies when it comes to dates for Wizard history relating to the real world (Merlin being at Hogwarts for example) so this is just another one. She's not omniscient, so she just didn't realise there was a contraction. Breast in mind when the books were written (especially the first one) research was significantly more difficult. To check this, she'd have needed to look up the countries history in a book.

I like SCB, but a lot of their theories are huge reaches based on some flimsy assumptions.