On point 1: this is already available in v4.2.0. The hide-whitelisted button in the duplicate tabs footer makes the "Close duplicates" button skip whitelisted tabs, regardless of whether auto-close is on or off. New Tab and about:blank pages are also excluded from detection entirely, so they will never appear in the list or be affected by "Close duplicates".

On point 2 (notification on duplicate): the "Open popup on duplicate detected" option in the Options page already does this. When enabled, the popup opens automatically each time a new duplicate is detected, so you are immediately aware without any automatic closing.

On point 3 (choose new/old/nothing per duplicate): when the popup opens automatically (see point 2), you can see exactly which tabs are duplicates and use the X button next to any row to close whichever one you want. The global default for which tab is kept is also configurable via the Priority settings ("Keep older tab" / "Keep newer tab").