This is the case for a very simple reason:

Achievements are not for players, they are for analytics. The Achievement system is primarily a way to track player activity in a player-oriented fashion by establishing these milestones and data points as player goals.
A modded game may not provide accurate data, so that data collection is turned off.

The Flaws of Divinity: Original Sin II: A list of observations of the game's shortcomings for the community.
Found HERE.