maybe so. but as you said, they would still have gotten some sort of money for it. its at around 3.4 million at steam spy alone. obviously sales and promotions have helped this one leg out a lot. but even at a low price, at 11 million its probably a very profitable game.
I find it unlikely that it was very profitable, because then Irrational Games would have been ordered to make another sequel. Also, I've read an article last year that was dealing with the subject of IG's drastic downsizing and the (former) employees that provided statements said that the internal sales expectations for BI weren't met. They kept the studio running until it became clear that the game wouldn't leg it out at a high enough average selling price, so a lot of the staff was laid off.
Of the 11m copies, only a small chunk was sold at full price. BI was in development for five years and had a big marketing push, so the costs of the game were high. I don't think the game lost money for Take Two in the end, but it's a case similar to EA's Dead Space 3 statement that a franchise isn't worth continuing if you can't sell 5m copies (that number is obviously before big discounts are being offered).