The "una cuм" debate is simply, uncharitable legalism, like the Pharisees of Christ's time would invent to divide the people and keep power over them. In particular, Fr Cekada's article on the subject (God rest his soul) is historically, liturgically and logically wrong. The whole idea is a Sede power play to keep the laity in the pews.
The prayer itself mentions "and all orthodox believers". So...if the pope/bishop you are praying for aren't orthodox, then even if you mention them, the prayer doesn't apply to them specifically, but only to their office. It's so simple there doesn't even need to be a discussion.