Those numbers aren't really comparable, because the meaningful decision you can make is between "getting vaccinated" and "not getting vaccinated". If you don't get vaccinated, you still might not contract COVID, and if you do contract it, the chances are pretty good that it won't be severe enough to ever be diagnosed by a doctor. So that 1000 micromorts is estimated from a subset of people whose outcomes were significantly worse than average.
I still think it's almost certain that, for a typical healthy person, getting the vaccine is by far the safer choice. (And that's before we even start worrying about non-fatal outcomes such as long COVID.) But the difference is probably a lot less than the 3 orders of magnitude you're suggesting.