Better With Mods has a feature called HC Strata, which changes the mining level of stone as you dig deeper down. Exchangers don't account for the change in mining level from this feature.

I spoke with one of the BWM mods shortly and he said...
well if you ask them tell them to call HarvestDropsEvent and have a getHarvestLevel that is appropriate

Ofc it seems the exchangers already have normal harvest levels, so I'm assuming it has more to do with just the call to HarvestDropsEvent? Not that I know the internal workings of exchangers (just taking guesses). I'm sure you'll have a better idea of how they interact.

This is an interesting bug... I'll have to look further into that when I have time.

I think I've fixed the issue, but I am not gonna release the update publicly yet since I've still got a few stuff to add for the final release. Here's an unreleased build, try it out and let me know if the issue has been resolved or not.
Download: Click Here
You'll also need a new library mod called GunpowderLib for this build: Click Here

Confirmed; this is fixed in the version posted. I'll let you decide when to close this issue (in case you want it left open until you release a public jar)

Fixed in 2.9.