Okay so even though the tga's in the override directory that Aspyr are using appear to be totally normal tga's I had a hunch that they might be re-encoded with PVR-TC (Power VR Texture Compression), the like of which is native to the iPad families GPU's.
I recompressed a texture file to PVRTC as a tga file and placed it in the override folder. Unfortunately still no joy, just a blank black shader instead of anything being loaded in.
I also tried this with a tiny white 128x128px tga file I knocked up in Photoshop. Totally normal 32bit tga file and only 16Kb in size. I still got a blank black shader in the game, as though nothing was being loaded at all... The quest continues.
Just keeping you all up to date so no one tries the same things I am all over again and wastes time.