I read that as being that Trump is doing a favour for Stone, because he doesn’t need him for a political appointment. Flynn, however, is still needed because Trump will appoint him as before and he needs to be untainted in order to get past the Senate.
That’s how I’m interpreting Trump’s actions.
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.