So I've noticed that there aren't any mods that change this behavior. I expected that when hit with, say a lvl 2 affliction, a lvl 1 inspiration would reduce it to a lvl 1 affliction, not overwrite it completely. Is modifying this behavior something that modders don't currently have access to?

Unfortunately that behavior is driven by code, not data.  If an affliction appears in the HardCountersType of another one on the same character, it just removes both of them.

 

The status effect system is pretty robust, you might be able to get this to work by removing the HardCountersTypes and doing something with AfflictionResistance effects on the afflictions, but it'll be pretty nutty.