Interesting issue. It’s a tricky one for MODx, as it’s sort of built that way. And I’m sure it’s a great way to start an argument, just like the proponents of absolute paths vs. relative paths. Religion and politics are easier to discuss.
To be sure, I have actually made a number of MODx sites with no Base Href at all, but there are some things that I think pretty much require it, like using the alias path for SEO, and what Ryan said.
I can think of an unusual case just last week when I had to take it out. I was pulling in MachForm (third party form making app), and I made a nice little snippet that included it just beautifully, and my clients are excited because now they can make really nice forms fast without writing a line of code. As I recall, the "redirect after you’re done" part would not work with Base Href. I probably could have forced it to work by hacking MachForm code, but I took it out and all was well.