How about handling “macro from clipboard” this way:

Add a “Get Macro from Clipboard” command in Macros menu.
Use this command to set the “macro from clipboard” as the current macro (just like what “Select this” command does).
Now the clipboard change won’t affect the current macro.

Usage example:
Record a macro.
Edit to make it better.
Ctrl+A (or select a part). Ctrl+C.
Use “Get Macro from Clipboard” command.
Now I can run the edited macro, without saving it. And it’s better than just record-and-run-without-editing.

This way, the “(Clipboard)” item in “Macro Temporary Options” dialog is not necessary.

Alternative commands:
Run Macro from Clipboard (directly)
Run Macro from Selection (directly)
Get Macro from Selection
Maybe you could weigh them and choose the best solution.