How can I allow hotkey conflicts?
Eg.: both CUT and LINECUT with ctrl+x
It flags conflicts for you, but doesn’t stop you from having conflicts. When there is a conflict, Notepad++ will pick one of the conflicting actions and apply it. There is anecdotal evidence that it picks the first one it comes to when doing some list of processing, but you cannot control which one occurs. I even vaguely remember one case when multiple actions may have been taken, but I cannot guarantee that will work.
In general, it’s a bad idea to have conflicts, because you cannot control whether one, some, or all of those actions occur when you use the hotkey. But if you’re willing to live with the ambiguity, feel free to leave the conflict there – Notepad++ won’t stop you.
If you want to guarantee that multiple actions occur with the same shortcut, record a macro where both actions are explicitly invoked, then assign your desired keystroke to the macro rather than to the individual actions.