I'm aware of what System Preferences is. My point was that you didn’t mention which preference you were referring to your reply. Thanks for clarifying.
It turns out the preference you mentioned is not the source of the issue. Mine is set exactly as in your screenshot.
When Alfred's "Ignore thousands grouping separator" is unchecked, Alfred fails to correctly interpret 1,234 * 2.
When it is checked, everything works as expected.
Thus, my feature request is to default Ignore thousands grouping separator to on for all users.
I now know how to fix this for myself, so my issue is solved. I'm humbly suggesting that checking the Ignore thousands grouping separator box by default would be a usability improvement for all other users trying to paste numbers into Alfred to do math on them.