The sole purpose of a DOT complaint is to file one in conjunction with a chargeback and to thus speed one's refund. If DOT happened to bring an enforcement action against a carrier at some point, that won't affect your particular ticket.

The value of the DOT complaint, as most who use it have found, is that it is forwarded to the carrier with the requirement that the carrier respond to the passenger with a copy to DOT. That generates the refund.