As it happens, this restriction was lifted in Moodle 2.7 with the implementation of the Scheduled Task system and new locking API. The new Task system makes use of the locking API, which means that you are able to have cron running multiple times. In fact, we now encourage running it as frequently as possible and removing any external locking mechanism you may have had in place.
In this situation, any individual task which is currently running will be skipped by the other cron runner(s).
If you're able to point me in the direction of the documentation leading you astray, I'll make sure that we update it so as to reduce future complications.