In that case, couldn't the Stuka be given a specific damage table entry for UKF emplacements - something like 0.67x multiplier?
It could, but the game is already bad at communicating things to players and hidden modifiers should be avoided as much as possible. Anyway, the original point was that the Stuka in its current state is already very good against infantry and support weapons and even vehicles (as long as it doesn't get direct hits) and it's considered to be one of the best rocket arties - making it good against emplacements as well would simply make it become overwhelming.
The only thing that could be done imo is reworking it to be more like the Panzerwerfer (rockets get lower damage but deal AOE suppression) which would make it a lot fairer against infantry and team weapons (and giving OKW a proper anti-blob tool) and then moving the incendiary barrage to vet 0 or vet 1 and rework that into a garrison and emplacements counter. But those changes would be so significant that they likely will never happen at this point.