I could see it taking that long (discounting any prompts as mentioned) on a slow as molasses Atom, sure, but is that also the case on a real PC?
Sounds like the installation procedure wasn't thought out too well though if prompts to uninstall software etc are given that far into the process, they should really be right at the beginning.
Edit: from reading the article, sounds like it would've been quicker to install 8.1 from scratch rather than updating from 8 to 8.1...much like Vista's service packs which also take an age to install.