It's not like 3rd and 2nd SOLDIER classes were really that big of a deal, it was mainly just Sephiroth and Genesis. It wouldn't make much sense if Shinra didn't have his grubby hands on more things than just the G and S experiments.
Granted, there's a lot of Deepground's history that never got explained outside of the Japan-only and now discontinued DoC: Online. But you can read up about it here:
The Darkness of Shinra – Deepground’s History Revealed | The Lifestream
The way they implemented the idea of Deepground, and the fact that it isn't seen anywhere else in the compilation other than some really vague bit where they drag Genesis off, make it really lame. But it could have been great.





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