Three was seven personalities and at least two centuries ago. It's no surprise Eleven might pronounce a word differently.
Much more than two centuries. More like at least four to seven centuries ago. The Third Doctor never gave a straight up age, while The Second Doctor said he was 450 in
The Tomb of the Cybermen and The Fourth Doctor said 749 in
The Brain of Morbius. Then you throw in the variety of inconsistencies throughout the show, especially since it returned in 2005 because The Doctor has been to known to lie about his age on a number of accounts.
The above geek rant aside, you make a valid point. Perhaps it's been so long since The Doctor has even
thought of Metebellis III that he forgot how it was pronounced.