In the doc you pointed to, I believe you should also mention that all the URLs pointing to the MEDIA folder, should be updated as well since the custom.css file is at a different level than the original theme style folder.
Also, this way, how do you target multilingual pages? In the original theme there are two versions of each CSS file: for LTR and for RTL... which should be copied into the custom.css file?
I believe this is an issue for a separate thread...
Thanks!
Emanuel.