You can add a blurb in appropriate places to let the user know about the functionality difference. Where you can currently edit the notifications...
Trigger push notifications when
[ ] Online, away or offline
[ ] Away or offline
[ ] Offline
Notification alerts are only pushed to your mobile device when your online status matches the selection above.
Change the second option to:
[ ] Idle, away, or offline (idle only available on desktop app)
I personally don't see anyone ever wanting "Away or offline" when "Idle, away, or offline" is available, but if some people want it kept, you can always have the four options. For non-desktop-app users, the "idle, away, or offline" and "away or offline" options would be synonymous.