No problem at all!
1. The stack when selecting: I see. It sounds quite complicated for me haha, but I think I get the idea. Many times I think Ren'Py works just like CSS/HTML, like how the background(-image) and the image(img) are different.
2. Sorting the stack: I can't think of any new ideas for now, but I think making it as close as how it visually looks like would be more UX friendly. In this case, the buttons which are in front of the background is stacked first, and the background is stacked later. Depending on whether I understand how this tool works, this suggestion may or may not work.
This reminds me of how Ren'Py's native inspector tool (Shift+I) is displaying information.
3. Going all the way when trying to select in the opposite way: I think this is related to the first two topics. 'n' and 'm' to move back and forth sounds interesting, I wonder how hard it is to implement it. Probably not hard? XD
4. Rough pos: aah sometimes when I just want to move a few pixels, I just change the number manually myself. I know I could have used the tool to shorten this process. Like, looking back, isn't this tool meant to speed up that process? Integrating this tool to my Ren'Py coding is very new so I have to adjust that workflow... I guess it's time to familiarize myself with it. So, nevermind haha. >.<
And thank you for playing Ice Cream Culprit!! I hope you get a nice ice cream (or any sweets) of your liking as well haha.