I don’t know, you could try to change
config.rb accordingly, but this is potentially a source of odd bugs. I’m not sure why is this a problem, since usually
source has more subfolders, not only
layouts but (in my case):
localizable (in case of multilanguage projects),
partials (I still prefer to have them in subfolder). I’m pretty sure when your project grows, you will have more subfolders.