I think that the answer is not that they will be confiscated if not in the original container, but that there is a better chance that they might be confiscated.

Technically, prescriptions can only be carried in the original labeled bottle and this seems to apply to medications in a form that would not otherwise be prohibited, i.e. tablets. If you have tablets that you cannot demonstrate to the TSO are not prescription, they may be confiscated. Then, again, they may not because, of course, non-prescription tablets are generally allowed in your carry-on in any quantity.

When the rules make no sense, it is awfully hard to interpret them.

-- Suzanne