Actually Achievements are an odd duck. For many players they are indeed of great value. It digs into that whole "collector" mentality.
I mean "gotta catch em all" ala Pokemon.
There are people who love to Collect things. I mean there are people who play the most horrid Steam games just to get another level or another "card".
There are also a lot of players who just don't care, but the Collector Mentality is too big to just ignore.
So, to ensure that an Achievement has some "value" to these collectors, its not uncommon to say no to Mods.
Yes, a good middle ground would be "flag" certain mods that would say prevent you from getting Achievements.
I personally could care less about most Achievements, but I do understand WHY there is an obsession with getting them.