I think everyone agrees that when done right, fixed layout is beautiful.
The problem is that it's so hard to do right because no one fixed layout works for everyone. The author you're quoting is talking about fixed layout for iBooks in general and the iPad in particular.
That's a valid target, because there is only one form factor and two resolutions to target, and the higher resolution is simply twice that of the lower. You can do a fixed format for that platform and expect it to work for the vast majority of readers.
What you can't do as easily, if at all, is throw that same fixed layout into the Android wilds where it has to face a much larger range of resolutions, sizes, and pixel densities.