"on top" window flag is unfortunately is not accessible to Chrome extensions. 

So this behavior is only possible using the external system utilities to manage window.

Sorry, not very well understand your problem. can you formulate it differently?

For example you said that

"action of tabs to be closed but listed in TO is completely forgotten."

What actions is forgotten?

Maybe try to explain this issue as serious of steps - what you do, exactly, what you expect after you do that, what you got instead.

Cool! Thanks! At least they notice it's again. 

Cannot reproduce this, what is the OS you use?

The problem with auto-scroll in up direction is unfortunately a Chrome problem, and even more, it is the regression, it was work in previous version. Please star this issue to bring some attention to it:

https://code.google.com/p/chromium/issues/detail?id=227728&can=4&q=up%20direction&colspec=ID%20Pri%20M%20Iteration%20ReleaseBlock%20Cr%20Status%20Owner%20Summary%20OS%20Modified

as it is seems that the Chrome team does not think it is very important to fix this issue.

>  cloud solution is probably more work to realize. 

Really so, but i hope to finish soon.

Until that, unfortunately, only the most critical bugs will be fixed (and unfortunately so is happens with every new Chrome release....).

That is how it is expected to work.

try to organize your saved windows in the beginning of the tree. Not in the end. The proposed change just create much more problems actually.

One more way, Chrome only.

Select all the tabs in the original Chrome tab strip (by shift click) - then drag them all to the tab strip of the target window.

One other way

Place a group, drag both windows to it, save-close them both, delete the saved windows nodes (they must not be collapsed). Double click on group - it will open as the window with the tabs from both of the deleted windows.