Wait a minute. You are conflating aircraft certification with pilot certification, ratings, and proficiency. The two are vastly different. When I train for a new rating in my RV-7, I am developing and maintaining a particular skill set. When I go find a DPE to evaluate my skills and sign off my new rating, I'm not asking him to certificate the aircraft I used to develop the required skill set.
I understand that there are many pilot examiners and instructors who choose not to give checkrides or training in experimental aircraft. That is their right, and that is why the requisite placards are there. (I'm "just" a pilot, and I won't fly in any Light GA aircraft that I haven't at least had the opportunity to walk around and take a close look at, unless I know the folks who maintain it. I might even ask to see the books.)
The idea that I should be precluded from training to a new set of skills in an airplane I own, and in which I intend to use those skills is asinine. If the airplane is equipped as required, and otherwise maintained and operated within the applicable FARs, as an owner, I should be able to use it for training. In fact, doing so is a logical requirement of safety.
...and yes, this did all come about as the result of one for profit Warbird operation using the training loophole to offer joyrides. If you are unfamiliar with that case, perhaps you should become so before making broad generalizations like suggesting that pilot certification and aircraft certification are remotely the same thing.
The school scenario you imagine is not really the issue at hand. It's you extending the discussion so that you can convince yourself that you have a point to make.
Personally, as someone who is engaged in some additional training at the moment, I've applied for an owner LODA under the new rule, and I am going to be patient and see how it all works.