For now you can use workaround software/scripts for saving window position based on window title.
It should be quite possible to find or write one which will save window positions by polling current ones and will restore/reapply when appropriate.
Though there will be some bugs, cause using title text as ID is not the best choice, some sites do not provide needed distinctions in some cases, for example
There is easy enough workaround for users who want help in a new window - click on "?", then on "Print" button which will appear at the top of help section. Press "Cancel". Voila.
> hotkey is impossible without embedding a script on every page, which will require access to tabs content
Actually, you can now make hotkeys for "clicking" extension buttons. (look at bottom-right corner of chrome://extensions) So i guess It's an easy workaround (even if it will require additional extension for this feature)
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Then you could make permanent rule to hide TO tabs and windows, maybe don't show parent windows of popouts since there is only one tab anyways, and find all the things you wanted to do on that project, without scrolling