New Teacher and Style
FYI: I have seen Chiba Shihan from the Western Region, USAF, use both (the middle-knuckle strike and the sankyo on the chest) of these variations in his technique. He's both a Hombu uchideshi under Osensei and an Aikikai pillar.
This middle knuckle strike is also quite common to differnent type of Karate. I think closer investigation would lead you to discover that it is in fact not an inherantly weak strike. Of course you have to know how to make this type of fist, just as you would have to know how to make any type of fist, in order not to have your hand injured. So aside from asking your sensei where and when this type of atemi should be thrown, you might also want to ask her/him exactly how one goes about making that fist so that it is not open to self-inflicted damage.
Just a thought,