I train some with a Nishio influenced sensei myself and at least in my experience, it's not that the Nishio style throws out the L shaped hanmi stance but that in certain situations one moves into an iaido-eseque parallel stance as a part of the tai-sabaki. One example being Yokomenuchi shihonage/ and or iriminage. Nage begins in hanmi but the rear foot moves into a parallel position(a la iaido kamae) before the front steps back while Nage cuts down/redirects the attack with his/her arms. But that is just from my experience. I also originally came from a dojo that used the foot turned out stance which you referred to as stance 2 in your first post;the dojo-cho was a former kenshusei of Chiba sensei. I totally agree with Joe in regards to this stance. When your hip is flexible it is very stable and quite safe for your knee but if you have tight hips it can put a lot of undue strain on the knee. This might be the reason that the dojo-cho from my first dojo does a lot of yogic hip opening exercises at the beginning and end of class.
Thanks for the pointers Chris. I am still figuring out exactly what I'm meant to be doing. I just know that there have been a number of instances (such as the ones you described) where I have had my footwork corrected. This has been particularly pronounced whenever I have been holding a sword. Having said that, my weapons work is particularly rusty because I spent the last 4 years training with a student of Masatake Fujita who was famously quoted as saying "weapons practice is not part of Aikido". My sensei didn't necessarily agree with this statement, but he simply didn't teach weapons because he had never been taught.