My opinions,
on the ground you have times when no one is in the cockpit nor the Apu ground control panel. So, when the loop detects a fire it just shutdowns the APU and extinguishes the agent.
In the air, there may be different scenarios where the automatic shutdown and agent extinguishing wouldn't be wise (may be). And knowing that there is always someone (hopefully
) in the cockpit the designers did not intend to do it.
Just my thoughts....
Guclu