I might have been, yes. Is this not supported?

To clarify: MySQL (5.0.95) does not return the value when queried, instead it gives an error, which causes the setup warning checker to crash and bring down the entire request with it. Phabricator's homepage fails with an error message. I can't ignore the setup warning because it isn't even shown (there's no UI, only the error message on blank page). This happens both before and after adding the option to the [mysqld] section of my.cnf.

On my (relatively old) Phabricator install, this issue-check caused Phabricator to fail with unknown system variable 'ft_stopword_file' after upgrading phabricator.
I had to hunt down the specific file and comment out the check for this and for min_word_len which results in a similar error.

Doesn't happen only on empty lines. In my installation this shows also on some other lines -- specifically the first few lines of each file, up to the first opening brace (this definition is not rigorously tested).