The players invited to the combine are the ones teams are considering drafting anyway; all the 40 times do is move players up or down the list by generally small amounts. The point isn't that 40 times are useless, it's that they provide very little additional information about a player. Champ Bailey was going to be a high draft pick no matter what he did at the combine, and everyone already knew that Trindon Holliday was fast but probably too small to succeed in the NFL.
Likewise, someone with a 3.9 from MIT or a bunch of good open source work who's coming for an in-person interview is already qualified, and the whiteboard doesn't tell you anything new. I'd guess Google sticks with them for the same reasons teams tout 40 times - it's good marketing both internally (making decisions seem less arbitrary) and externally (look how tough our interviews are is a more socially acceptable way of saying look how smart we are), and it allows people to deflect blame if a hire doesn't work out. Judging by the number of posts about Google interviews I see here and elsewhere, the marketing is certainly successful.
Also, I think your view of the interview pool is somewhat skewed. Most of the candidates I see do not have 3.9s from MIT (BTW, I believe MIT has a 5-point GPA, so it really would be 4.9), and a lot didn't go to Ivy-League universities.