I agree with what you are saying. Apart from anything else, if a person is only training eye gouges, groin shots a) are they likely to be able to do them when the heat is on? b)are they likely to be successful c) are they going to be an appropriate technique to the situation at hand?
I've gotten back in to Judo since last year, really as a way of getting a workout thats a bit different from my normal fitness routine. I've recently started trainig a bit in a local Gracie Garage too. I'm sure you know the sort of place I'm talking about, they train in a garage using the Gracie Academy material.
One thing I did notice is that they use BJJ against different sorts of energy. For example, they use the basic trap, roll, escape while someone is simulating striking or a two handed choke from the mount. Althought the principles are the same as in any other BJJ class, you're training against different sorts of movements.
Most combat sports, be it BJJ, Judo, Wrestling, Boxing et al... usually only focus on defeating other people from the same discipline. I think it could be useful if now and again a judoka or wrestler learnt how to defend against a partner who is trying to punch them in the head, or for a kickboxer to learn how to cope when someone clinches you and tries to grapple with you.
In Judo they talk about high percentage throws and low percentage throws. High percentage throws work most of the time in Judo matches. Low percentage throws rarely work in Judo matches. In the same way, I think in physical self protection, some training is high percentage (likely to work) and some training is low percentage (not likely to work). For me things like eye gouging and groin shots are very much in the low percentage category.
"Let your food be your medicine, and your medicine be your food"