Another really irritating result of lining everything up just so is that when you do a search+replace on a bunch of code, and change the length of an identifier. Suddenly you've screwed up the formatting on a bunch of tables without even knowing it! This is especially annoying with doing a search+replace across multiple files, with lots of code.
That's not to say that lining things up sometimes is a bad thing, particularly when you really have a table (e.g. initializing a big array of structs). Sometimes having things lined up makes it easier to edit later (e.g. using Vim's visual mode). But I'd say that 90% of the time, it's a waste of effort that could be spent, say, making your code actually work better, rather than look better.
In certain revision control systems, one doesn't keep differences, but whole objects, so the point is moot there unless you have some serious bandwidth concerns.
I'm quite disappointed the article doesn't mention that.