That's how sights work in EFT. In the video it didn't look like you were doing much to control the recoil. It's not weird interaction, more weight in the rear = more muzzle flip, makes perfect sense. Weight does also reduce recoil. The stock is going rearwards into the shoulder as it should. Stock not changing pistol animations is just how pistols in EFT work. It's still useable in your configuration, if you want more recoil control then you need to choose a lighter magazine.
You know what, I guess I was complaining about nothing. Just tested the Glock18C in vanilla EFT and it was equally a bad idea to use a sight on it in full auto because the bullets just wouldn't go where you thought the reticle was since it would jump all the way out of view.
The stock could do with a bit more dispersion reduction judging by the videos I've seen of people full autoing the glock with the stock, but honestly I'm at the point where I'll just make the adjustments myself once I find the right files to edit.