The machines are placed outside of claimed areas (FTB Chunks claims). but do not break any block.

The Auto Placer, can place blocks in these same areas without issue.

The issue lied in the isCorrectToolForDrops check... since the fake player of the Breaker doesn't have a tool it could only break stuff like dirt.
The vertical digger didn't have a tool either, it was checking if the block it's breaking was able to break the block 🤔

Fixed in 1.3.6+mc1.21.1

This is working pretty well, I did notice it doesn't appear to want to mine dirt though.

Like, it dug or a huge area underground but left dirt Blobs wherever it found them

Well, this comment doesn't exactly inspire confidence about the breaker working correctly: //TODO might double check this is right mikey