So a couple of versions later now, has any of this been implemented and if not, are there any plans for any of them in the future:
1. Tray icon flash disable (preferably by default, but at least an option).
2. Flush Clip History, as a 1-click option on the main menu, right above where it says Exit.
(Probably the most important request, since Flush Clip History would get rid of copied credit card number and other sensitive data someone might be temporarily working with.)
3. This should be default: Misc. Options 1 > CHECK: Update clip modification date on paste.