In that case (excess from Capt to F/O on same aircraft) they could still flex, they would be F/O flexes. They would also still have the experience of actually operating as a Capt on the line. Their excess has nothing to do with any F/O getting a left seat qual and/or PDO bumping line Capt's.
The fact remains that those who think F/O flexes getting left seat qual's are negatively effecting seniority/numbers on the line/excesses/etc are way off.