@TimO Yep, that sounds right. It will probably be quite common that the micro will have more capabilities on the various MYSX pins than the MYSX spec states the pin in question can handle, but I tried to spec MYSX to be as compatible as possible with a range of micros so it is quite "stupid" in it's pin featureset.
It is basically the same reasoning for the connector. It is large and bulky and hard to use in really small boards, but I wanted it to be easy to use, and easy to source. And it provide a nice debug interface when left unconnected. Tradeoffs, tradeoffs.