Okay, I see that your parts are not overlapping at all, my example they still overlapped in one plane. For sure that's a major issue with the Measure tool. Seems like the "Measurement indicator" should start at the Pick Point of one of the parts instead of coming off the edge OR better yet it should be something like what SolidWorks has:
YES! Most of my design work is top-down. Why would anyone want their main part locating Constraints to break when they use features of the software that are intended to make things match up?
I think I see what you are talking about, but am not sure. I do a lot of top down design stuff, so this should be something I like, but I am not sure we are all talking the same thing here