IPFS is a decentralized file store. It isn't a decentralized website host, although it can be used as one. That is just a nice consequence, not its reason for being. IPFS is a building block. If you want a better experience, build a tool that takes advantage of IPFS.
I think this comparison is pretty good: the author's problem with absolute URIs is essentially the same as using `file://` URIs and accessing the site from different directories (although `file://` doesn't have the chicken-and-egg problem of pages trying to link to their own hash; IMHO that would be worse than relative links anyway, even if it were possible).
Still, I think that the author's criticism is valid, since the IPFS project does seem to encourage the view that it's suitable for Web hosting, rather than just "a nice consequence". The author's struggle with IPNS, and recommendation that it be de-emphasised in the docs, is in line with my own experience.
The IPFS documentation only provides a "basic example" of hosting a website with IPFS. In general, the IPFS website focuses on its uses as a file system.