Calamity not affected by Abnegation, but Refraction is

Is there an underlying mechanic here, or is that just the way it is?

I believe Calamity is unaffected by any other abilities at all, due to potential abusiveness.

Not sure if it’s a bug, but I found at least one thing that affects Calamity: Intimidation.

Can’t a Bone Reaper’s ability stop Calamity?

Abnegation stats that your creatures have “additional attack, etc…”
Meaning that the value is not changed but you have an additional value that is added only at times. For attack that is when you actually attack. Refraction however only triggers when you actually use defense as intended (as in vs an attack) hence why it affects that but not calamity.

Any ability that increases your actual attack value instead of “having additional” of said value will work for calamity. Inspirit comes to mind.
As i have noted aditional basically means its only counted when attack is resolved (including defense and anything that triggers as a result of an attack). While anything that increases a value always works, because it is permanent for the duration of the combat. Hence it works on abilities that trigger as a result of something else than an attack. (Like calamity).

And yes, bone reapers stop calamity.