I'm using PKHeX version 23.12.22.
When I generate a raid encounter Pokémon from the encunter database and manually adjust its height or weight, it is flagged as illegal.
However, after I enable the shiny flag, it is considered legal, regardless of any further adjustments I make to the height or weight.
Additionally, the stat nature remains unchanged when I generate a Pokémon from the encounter database; the nature is randomly determined correctly.
I've attached two sample .pk8 files to reproduce the behavior.
0350 - Milotic - EC9B0698687B.pk8
0350 ★ - Milotic - A3D80698687B.pk8