It poses a problem for deployment, collaboration, version control, etc. For instance, a new data type (not a problem in WP, but you could substitute meta fields

It poses a problem for deployment, collaboration, version control, etc. For instance, a new data type (not a problem in WP, but you could substitute meta fields or something) will frequently require some new code as well -- a widget, template, or whatever. Once I've built this in my dev environment, tested in the staging environment, and deployed live I will have had to set up the new data type in three different places, or written a script that does it, but most CMSs don't provide those tools, so you would be stuck hacking around with internal functions that might or might not be stable. Meanwhile, any other developers will then have to replicate the same changes in their dev environment. Version control exists to solve these problems, but when this stuff is stored in the database it is a lot harder to consistently reicate changes. I'm sure people come up with solutions that don't involve replicating configuration in the GUI, but my point is it should be baked into the CMS.