Atom and Core/Xeon don't share microcode? e.g. vulnerabilities in one would never work on the other?
No, the microinstruction formats are very different, so also the microprograms must be different.
Even the newer Atom cores, e.g. the Tremont cores from Jasper Lake/Elkhart Lake/Snow Ridge/Parker Ridge/Lakefield have a different microinstruction format than that which has been published now.
For every generation of Intel CPUs, reverse-engineering the microcode requires all the work to be done again, what has been discovered for another generation cannot help much.
While these are reasonably widespread in the cheapest personal computers and servers, the impact of examining their microcode is much less than if the decryption keys for some of the mainstream Core or Xeon CPUs would have been obtained.
In a more decent world, the manufacturers of CPUs would have been obliged to only sign their microcode updates, without also encrypting them, to enable the owners of the CPUs to audit any microcode update if they desire so, in order to ensure that the update does not introduce hidden vulnerabilities.