minecraft and world of goo both come from
"indyprogrammers", that made many experiemental gameplay demos.
So they have a well funded programmer background anyhow.
Having your own engine lets you have more power over the
design and features. (no workaround looping back and forth)
But I think they are special cases.
Torchlight was done in Ogre for example.
i don't think they are exceptions. i admit that i didn't do a thorough search but the biggest indie hits of the recent years that i quickly found all used their own engines (often a combination of several open source libraries). to me this kind of questions tools like gamestudio and unity. this shows that to be successful you first of all need to be a "indie programmer" and not an artist with nice ideas and tools that claim that you don't need to be much of a programmer.
