Custom origin replace is set to true and order 0 and In game, at selection window... they are stilll appended to default ones.

Could you send the datapack here for testing purposes?

Incredibly strange. I can't seem to replicate this in my environment.

My guess is that the base origins have a chance of being loaded after your datapack. So my suggestion would be to plop a loading_priority onto it.

This'd look like

{
  "loading_priority": 1,
  "origins": [
    ...
  ],
  ...
}