Regarding the original issues:
1. you can edit the references after adjusting the diameter, you have to just re-select the hole center manipulator:



once you are there, you can edit them by just selecting new edges. Fusion will remove one of the other dimensions to prevent over-constraining the hole:

I agree that this is not discoverable, and we have been discussing this for a very long time, and haven't come up with a great way to make those references easily editable and still preserve a nice smooth workflow in the most common cases. Today, you can select those references without having to go back to the dialog. So, you can just pick the face and two edges. We discussed putting selection items in the dialog for the edge references, but then you would have to go back to the dialog to enable those selections, so in a lot of cases, the workflow gets a bit more clumsy.
2. I was not able to reproduce the problem in your screencast where editing the hole feature shows the wrong references. It certainly looks like a bug - if you happen to have the model around, attach it and we'll take a look.
3. I was able to reproduce the third issue. I'll file that bug. However, there is a way to get the pattern to work like you want. It is a bit subtle. In your screencast, you have "Pattern Faces" selected as the pattern type. This should work, I believe. But, what I think you really want is "Pattern Features". Face patterns are an optimized pattern compute that just copy the selected faces around, then join them into the body. It is fast, but sometimes behaves differently than might be expected. Feature pattern actually reproduces the feature recipe for each instance. I tried it in this case, and it worked OK:

Jeff Strater (Fusion development)
Jeff Strater
Engineering Director