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.
A colour does not a painting make. That is definitely a valuable aspect of steam achievements, and would be an explanation why they've started out with them turned off with modded games. But they themselves do not warrant lowered user satisfaction when there are perfectly fine analytic tools available to developers that do not need such crude systems.
