Sorry about the delay. itch.io was down.
Ok. I see that some of my design decisions are leading you to these questions. I'll address them one-by-one
The stack when selecting
When you start selecting something, the tool gets everything that is in the 2D plane of the mouse. In other words, regardless of what is on top of it, it gets everything that is part of that position on screen. That is done by Ren'Py's internal undocumented API.
Think like you have an A2 size table with lots of A4 sheets of paper. Then you get a knife and pierce through all sheets anywhere on the table. The ones the knife pierces through are the ones part of the stack obtained. That's basically what this does.
The background image (more exactly, Displayable) is just an image like any other, for Ren'Py. There's no way to distinguish. Also, if it's always covered, it would be impossible to select it without hacks or annoying processes. So I ended up going with this process.
It is both not trivial to know when the thing you selected ended and when the next thing starts. It is possible to have some tricks that usually work but not in the rare times which is usually when it's most frustrating.
Sorting of the stack
The way the stack is sorted is just a UX decision I did. It had to be sorted in some shape or form. I decided to go from bottom to top due to how the levels look like and are build, so it's increasingly "upwards" when looked at in the UI but also, first select the "closest" to the mouse. If you have a better idea, I can take it into account.
Going all the way when trying to select in the opposite way
When I need that, I usually just press Esc and then m again. However, rule of thumb with this tool is to edit 1 or 2 things at a time and then edit in the source code which makes it reload. However, in this case, it seems like what you want is to move the button and then the text, for example.
One thing I can consider is that if you move more than some small amount or some time passed, the next to be selected resets to the first one when you press, in this case, m again. Would that help? Or would having a button to go the opposite way help more? Using n while in move mode, perhaps?
Rough pos each time
You mention:
The tool helps me getting the rough pos each time
The tool is designed to get the exact position you want much more fast than with editing in your editor and reloading. Is it failing to do that for you?
Offtopic:
I read the Ice cream culprit. It was really good and funny! Keep up the work! I'm a fan now.