The most important thing is that your arrow clears the shelf, regardless of whether you gain or lose anything by nocking lower. You will never shoot well with a bow if the arrow bounces off the shelf.
I find that as I nock higher, the bare shaft reads stiffer. That is, if I nock higher, I will get a little more nock right or less nock left than if I nocked lower. I assume this means that the lower I nock, the more of the bow's power is transmitted to the arrow.
I don't really think there is a significant loss of power from nocking 1/8 or 1/4" higher. Maybe there would be if you nocked an inch higher, I don't know. It is primarily a useful tool for tuning the arrow. For example, I was just tuning a bow today and it was a little nock-high, and also a little nock right. Ordinarily, I wouldn't worry about a little nock high. I might even purposely move the nock up a little if my arrows seem to be hitting higher than I'm used to. However, I thought I could get rid of the nock right and the nock high at the same time if I moved the nock down a little, which is exactly what happened. For this bow, the proper nock point turned out to be 1/2", which I think is unusually low for 3 under. For all my other bows, the lowest nock point I have is 5/8", and some are 3/4". So I agree with your comment about needing a little higher nock point for 3 under.
I've never shot cock feather in, so I can't comment on how that relates to nock position.