The deep insertion is for better isolation, but you do need a good seal as leaks will cause a low-frequency roll-off. Any verbiage I've ever seen about the bony portion of the ear canal was in reference to isolation, of which Etymotic does get a bit more (verified by third party labs).
As far as frequencies go, deep insertion will have a pronounced effect on the upper mids and high frequencies, however. Insertion depth makes a big difference. Shallow insertion will yield an overall frequency balance that is different than you would get with a deep insertion (and different from our published graphs). So the tonal balance does shift when it's pushed in deeper, which may be what some folks are describing.
When I was at Etymotic, one of the primary complaints we got from customers was that it didn't have enough bass. Many of these customers simply weren't getting a good seal, so I am sure it did sound pretty bad. Many, if not most, were happy once they figured out how to get a good, deep seal. Of course, some folks understandably want more bass, even when they do achieve a seal, which is fine as well.