Tier 6 inferium seed drops one inferium essence when harvested by machine (both gentle and breaking). Mystical agriculture's tier 1-5 inferium seeds drop 1-5 inferium essence as appropriate when harvested by machine. (User harvesting produces 6 essence as expected.)

Minecraft 1.12.2
ATM3 4.4
Mystical Agriculture 1.6.5
Mystical Agradditions 1.2.5

Is it the actually additions machine?

Cyclic's harvester (for gentle) and one (for breaking) from another mod that I can't remember off the top of my head.

Interesting, might be because I forgot to update the crops with the new getDrops method. I'll have to test it out later

I have the same issue with the actually additions farmer

Just tested and the change I made seems to fix it \o/
Hopefully I can get a new release out soonish