I shall look at this for a future release. Do any users reading this have any reason why they would want separate configuration on different devices? (e.g. use iPad for work and have a different set to TODO keywords)
I think syncing config files via iCloud is a good idea. Is there a way from scheme to access the device name ("Bill's iphone" or "old ipad mini") or some other identifier so that if people wished (though I can't think of why), they could use their init.org scheme code to make settings (as you suggest) that for whatever reason depend on which iOS device is in use?
Maybe an equivalent to Emacs's custom-set-variables would work for beorg. An init-custom.org would be managed by beorg and then read before a users init.org so that variables could be overridden programatically if required. Scheme access to the device name and model could be provided to allow overriding these on a per device basis.