I don't understand the notion that yonkyo, nikkyo and sankyo aren't supposed to be painful. That's what they are for! The pain isn't the only component in completing the technique successfully, but it's most certainly a large part of what makes it successful.
I don't want tendinitis in 5 years. lol
Don't get me wrong, I do do joint manipulations, and I do apply the crunch.
Other than that, sometimes you can't do a technique.
Example, what if you go for sankyo and notice the guy has made a fist. You are already committed to that sankyo, so you must act in that split second.and complete that sankyo. If you were taught to put emphasis on the ballance and center cutting off the bat, it is not a problem, sankyo still works. If you rely on pain alone I believe you are doing your aikido a disservice. In my little opinion, relying on pain compliance can become a crutch.
I've worked with a person before that relies only on pain compliance. When the pain compliance doesn't work, they try to muscle through, which can hurt some one seriously. Because all they ever learned was to apply pain to protect themselves, they have no back up plan. But they do have full blown tendinitis from a decade or more of taking those techniques.
The ideal is that all techniques can be done without doing any harm to the attacker.