Hi David,
Sorry for your trouble. The docs are actually correct, it was just that the Framework skin had been updated since the docs were written and the skin.less and it's import in the main.less were missing from the repository.
I've added the skin.less and the import for it to avoid further confusion in future.
LESS works very similarly to CSS in the way it cascades, so placing the Bootswatch files at the bottom of the main.less will achieve the same results, the reason the documentation states to place it above the skin.less is so that you can place any custom styles for your theme in the skin.less but it will still respect the Bootswatch variables and be the next cascade for any styles you wish to override.
There shouldn't be any issues with the Boostrap/Bootswatch versions as they are the same major version. If you do let us know.
HTH,
Elijah