One more easy workaround and option - simply ignore this "garbage" ; )
It is not harm, and can even serve as visual clues in you browsing workbook to remember what are you do last time or months ago : )

Yet as I say it was planed to fix already. Actualy even in high priority to fix.

TO sees them as crashed (and state that in titles of windows for such tabs), known problem.
This is because there is no easy and sure way to distinguish normal exit from crash (and sometimes normal exit is a result of unintentional system restart, for example because of some OS update)

This is known problem, and there is plans to fix this (i hope i will note diminish by this fix robustness and reliability through real crashes)

Meantime, only as workaround, I can only suggest closing all regular Chrome windows before TO window. So it will have time to detect that everything is really closed, not crashed. Because when all windows are finally closed TO is not able to save the state to disk anymore.

Yet i plan to fix this as soon as possible (donations will do a great deal in this...)

Can you problem be rewritten as next:

1. You have several open Chrome windows with tabs

2. You exit from Chrome by Exit menu item in some window

3. Next time you open Tabs Outliner its shows incorrectly detected as crashed windows, which was open at a moment of Chrome exit.

?

does not saw anything sub optimal. Actually you even not need to open Tabs Outliner if you have a window with one or two tabs. It is needed when you lost ability to observe tabs in current window. And in this case auto scroll works perfectly. And to change anything to satisfy complete strangers, with 3 windows and 9 tabs..., guys - sorry, you are simple not the my target users, why the hell you need Tabs Outliner at all? Is isn't it OS taskbar and default Chrome tabs strip are completely adequate and suficient for such cases?

Reread all of this and still cannot understand what you want  Some special behavior when only 3 small windows is present? then, something another when there is a lot other windows? I will not do this for sure.

You can open cloned view and use it instead of the main view. Cloned views does not have auto-scrolling behavior. Also there is undo scroll button to undone any accidental scrolls (including automatic).

Yet I will think about this option. Especially if it is collect really many votes. Really many people want this at first, but then they form new behavior and start to think that this is actually better to have auto-scroll. If this option will be available they will not obtain a chance to learn a really useful and productive way of use for this stuff, as most of them immediately enable this option.

It is planed. 

Meantime you can export you tree in some Google Doc document, along with all notes and marks, and share it between all you devices this way.

To export, all, firs expand all nodes, then drag root node to google doc, then you can undone nodes expand by clicking undo expand all.