I hope i can agree with you. But are you really sure? The period seems to indicate that the “unfortunate” belongs to the moderator action and not the flagging.
"[unfortunate statement]. Unfortunately." is idiomatic (if informal) English. "Unfortunately. [unfortunate statement]." is not, especially in this case where the second statement is parenthesized. If it was "Unfortunately:" or "Unfortunately," that would be different.
In my mind unfortunately can only ever refer to a previous sentence, not the next one. I read the period simply as a stylistic choice meant as a pause. They could have written it with a dash or a comma:
> [...] they tend to be flagged to death by users regardless — unfortunately.
> 1. Placement: “Unfortunately” is typically placed at the beginning of a sentence or clause to emphasize the regrettable aspect of the situation. It sets the tone for what follows and ensures clarity in your expression.
Sorry in advance if this is too much detail, but you seem to be interested in the nuance here.
"Unfortunately." here is a sentence fragment. It's idiomatic (conversational + informal) English to modify a preceding sentence with a sentence fragment. ("We could have some iced tea. Or lemonade.") There are cases where a sentence fragment can be used to introduce a sentence ("Delicious. I ate the whole thing.") but this is never an adverb (you can say "Unbelievable. You've done it again" but not "Unbelievably. You've done it again").
If one were trying to write "Unfortunately, there has been an error" with a long pause, you would write "Unfortunately... there has been an error", never "Unfortunately. There has been an error." The latter looks like a typo.
That's why (as a native speaker/reader of American English) I don't see any possibility of interpreting the text the way you're describing. Hope that helps!