I think that given some favorable global economics and if this "pilot shortage" actually happens this time, then the leverage will be in the Atlas Air pilot groups' favor for a strong contract.
I'd wager that there are fat times ahead at Atlas, barring some cataclysmic event that would throw us back to the middle ages.
Then it just comes down to what kind of career you would want for yourself and the lifestyle that suits you, be it here (5Y) or with a legacy airline and depending on all the variables it could be a difficult decision for some.
It ain't over 'till it's over...