I think Trump prefers to let the courts and appeals work their way through.
But Stone is 6 days away from prison during Coronavirus. That’s what is prompting Trump to act.
If Flynn was only days a way from prison, we’d see Trump act on his behalf as well.
You’re probably correct, but I think it is doubly important for Flynn to be cleared by the system, because if Trump can appoint him, he’ll be coming down on the intelligence agencies like the Second Judgement of Revelations.