Transmit Automator Actions Not Loading
So I figured this out after a lot of digging. In looking for the Automator action, I somehow skimmed over the application package in /Applications. 

Transmit's actions live in /Applications/Transmit.app/Contents/Library/Automator. 

Once I found them, I just had to clear the Apple quarantine info on that folder with 
sudo xattr -r -d com.apple.quarantine /Applications/Transmit.app/Contents/Library/Automator source.

I Hope this helps anyone with the same problem in the future!