Question One: This is not customizable, you have to click Yes or No for each note you open with the multi-tool.
Question Two: You can almost do this if you give a group of projects a name and save that group. Then you can just pick that group from the list. Saves some time but not as much as if Paratext were to remember the last group you used and Keeps it as the default.
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Question 3: If you are referring to how crowded the title bar can get if you share a note with many projects, then no that is not user configurable as far as I know. You should make a feature request if that is something you need. If it is related to the need for confidentiality be sure and mention that in your feature request. It would be nice if the multi-tool at least only placed the shortnames on the title bar.
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If I have misunderstood anything I hope others will give ideas how they deal with these issues.