There are a few issues at play here. Firstly, the CKeditor builds from the official site all have the config.js file with some default stuff in it, which means for anyone using a custom build they will get that default file and may override stuff they don't want.
A similar thing applies to updating Q2A as well - if we provide a default (blank) config.js it might get overwritten each time you update. Of course that applies if you modify the config in qa-wysiwyg-editor.php too.
The extra HTTP request for the file is a minor issue. So because some parts of the config are required to be in the PHP (the language and upload paths) I felt it was best to just skip the config.js file altogether.
I think you're right, allowing users to use the JS file would be easier. So maybe we can allow the config.js file to load regardless. We can start with a blank file (or better yet, move the non-PHP stuff from qa-qysiwyg-editor.php to config.js). This does mean that for any custom builds or when Q2A is updated, you'll need to redo your changes.
Alternative: I just checked and if there is no config.js file the editor does still load (I think in the old CKE it broke the editor). So we could provide no config.js and let users add one if they need custom config. This is better when updating Q2A since you won't overwrite your config, but you still have the same issue with custom builds, and you constantly get 404s if you don't have the file. I don't think this is a great solution.