They only have one version of each dungeon. So, no, you can't have the same dungeon with unskippable cut scenes in one case and skippable cutscenes in some other case.

But, you only need to run Castrum Meridanium and Praetorium one single time each per character. Any further runs are completely, 100% optional. So don't run the MSQ roulette if you dislike the cutscenes so much.
Should they ever remove the unskippable cutscenes, you should also expect that the rewards for those dungeons (XP, tomestones) will be massively reduced as well.