>  What's so bad about namespacing them in site.collections?

Because pages, posts, and data would be first-class citizens in Jekyll's eyes, but my collections would be a second class citizen (Not to mention, would make dogfooding 999x harder). 

User is in control of both site config vars and collection names. Assuming that a collection name is plural, the potential collisions you're looking at are plugins, layouts, gems, which I'd argue, collections could just overwrite, as those three in particular are rarely access in userspace.