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.