Different voltage sources across Vin and DC jack
wouldnt that then send current through the Vin pin and back to the coin cell battery? Is that what would happen in this instance?


Yep, that's right.


  shouldn't there be a design feature to prevent users from damaging it like that? Fool/fail safe?


No. VIN can also be VOUT. You can use it to power other things that want a higher voltage.