I think that's exactly it. Every Eagle is a Jaguar E-type restored. No different to a great number of vintage cars around.
With regards to Suffolk, I notice that the liquidator has confirmed there was a "threat" of legal action but no details as to the exact nature. The company owed nearly £800K to creditors, all of whom are listed in the winding-up order; I don't see any solicitors amongst them so I'm guessing no formal action had taken place. I'd guess that the company was already insolvent and any approach about intellectual property rights from JLR would have been the straw that broke the camel's back.
I like Suffolk Cars but I have to say I always wondered how they got away with it.