From my uses, I think it makes sense to default to presuming the user means every line. I'm not sure I know why a user, especially if they have a big clipboard stored, would expect it to land on line one only if they have multilines selected.
Perhaps you could put it as a checkbox in Preferences->Miscellaneous.
I've recently seen several other IDE boards, that use Scintilla, having this discussion and most seem to agree that the preferred default is to have multiline pastes paste to each line as the default.
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