That's very odd. I just tried starting a new save file and I can't replicate the issue with the base game premades - the Pancakes, Spencer-Kim-Lewis's, and Landgraabs are present in my fresh save.
The PSRO doesn't make any changes to the Grove or Gooseman households or to Rosie or Captain Whitaker. However, it does appear that none of the households that are supposed to have pets, have pets, including the Lynx household. I tried removing my mods folder and starting an extra new save and those households are still missing pets, so I believe we were both hit by an EA bug, most likely this one: https://forums.ea.com/idea/the-sims-4-bug-reports-en/cd-hr-disappearances-of-pet...
Please try repairing your game and see if the base game premades show up again.