Although, there is a small visual bug when $1 is not updated with recommended number. I will fix it a bit later today for inclusion to the new Virtualmin release. But again, just change it to 16 and it will just work.
At first you need to re-check and refresh configuration, and then when List Virtual Servers page displays actual list of virtual servers, users (Virtualmin Pro only feature) can perform mass update operation by checking needed virtual servers first and then clicking Update Selected button, i.e.:
That was a big clue. Once I did “Re-check and refresh configuration” all the domain names appeared. I first had to fix a bunch of legacy DNS consistency issues but once I had done so all the names were there.
Thanks also @Ilia we have the Pro version and can now do those bulk updates.