I use a custom Python language with a separate name than the default. I then disable the default python in the settings file, but it disables all subfolders in any plugin with the same name. Shouldn’t it only disable the top level** Packages/Python** folder and not Packages/SublimeREPL/config/Python as well?

I believe this could be classified as a bug. I would think if would have to explicitly defined as SublimeREPL/config/Python to disable a subfolder in a plugin. Though this is a very specific instance of how this has caused problems, I imagine similar issues could pop up in the future with plugins and the disable plugin setting.