No, it really isn't. If Apple really wants to force standard formatting on them, they can do what they did in the browser, and have a "readability"-type button. They've already solved this problem.
As someone else mentioned, they might as well use the browser to begin with.
You're right, it's a dead simple issue. I don't know what came over me, or all the other people discussing this with much sound and fury.
(Imagine, trying to avoid the typographical and layout nightmare that is the world wide web while you are trying to grow a business.)
Look, the Reader "solution" has many problems. Surf around and try it out for a while. Plus people are already complaining that it is an example of Apple's iron heel of "user experience" being forced upon the world. Oh! That's what people are saying about the iBook problem...
Apple doesn't need to and, frankly, is largely unable to curate the web. There's already lots of users who are used to dealing with poor design. This is not the case with books, or at least fiction books, which are not heavily formatted and typographically simple (we call it elegant...) People expect to just open them up and start reading and not have to figure things out. You start allowing complicated layout and interactive CSS and I guarantee you we'll start seeing book with navigation menus and other foolishness.
Apple is simply trying to make it dead simple for frightened publishers and weenie techheads to make a simple, commercially viable fiction book that users will tolerate while creators are learning about the finesse and subtlety of digital book design.
Either way this gets implemented, lacking a lot of educations on both sides of the digitally rendered page, there are going to be unhappy people.
No, it really isn't. If Apple really wants to force standard formatting on them, they can do what they did in the browser, and have a "readability"-type button. They've already solved this problem.
As someone else mentioned, they might as well use the browser to begin with.