A duplicate thread (Stock Takes Export doesn't contain Stock Items w/ zero inventory) has been raised for this, so if you voted for that one, please add your vote here instead. To keep everyone in one place, I’ve closed the other.
Following that other suggestion, would you just like one blank row per stock item? And so the site/location columns are empty? This would mean that you’d need to either fill in the site/location columns or delete the rows before the file could be re-imported.
And as @jason-weaver said on the other thread, you would need to be able to opt in or out of this on each stock take.
Finally, a workaround in the meantime is to take an export using the raw data explorer to get all your stock items.