Interesting thing is, traditional book publishers could do the same. Maybe they have, and we wouldn't be aware of it. My impression is that they mostly haven't and mostly wouldn't. I think Apple, Amazon et al. are particularly extractive, and they come at anything firstly from the point of view of how they can control and channel the experience, the level of focus being unique to them.
...Barnes and Noble’s budget electronic edition of Tolstoy’s “War and Peace” had searched for and replaced all incidences of the word “kindled” (a variant of the name of Amazon’s e-reader, of course, but also a legitimate English word) with the word “Nookd.”...
That wasn't by B&N. It was by a cheapass public domain parasite who did a search to replace "Kindle" (probably as in "Kindle Edition") and wound up FUBARing the book before submitting it to B&N.
And you don't have to buy your iBooks books from Apple. In fact, I rarely (maybe never) have, but I prefer it's reading experience to the Kindle apps (for whatever reason). I just use Calibre to convert.