This is NOT meant to be inflammatory, as I am EF user, but it is an interesting point.
There’s a reason EF isn’t listed in the article
One thing that I would note is that EF doesn’t keep everything in a proprietary database or SQL (or XML document), which is one of the main things the article is complaining about.
It builds actual Finder folders, with your actual files in them. The real life folders are in the same structure that you see in the application interface, which is not the case with Devonthink 2, as I understand it.
I do think the article is a good reminder to use Address Book, iPhoto, 1Password(or your manager of choice), etc when you do get a piece of information of those specific types.