If cutscenes are made skippable, then they have to reduce the rewards back to what they used to be, to reflect the time spent.
If there’s any kind of choice involved, then people will be in conflict.
Those who want to see the cutscenes.
Those who don’t care but want the full rewards.
Those who don’t want to see the cutscenes.
Those who don’t care but want to get through quickly with a lesser reward.

You will have people pressuring others to skip, whether or not it’s anonymous, or you’ll have people DC’ing or dropping out and eating the penalty in order to get the content they want, because there’s too many differing motivations there.
The only solution is to remove the choice form the instance entirely, placing the choice BEFORE you queue for the instance. You choose to enter an instance with cutscenes or without cutscenes, and you’re held to that choice.
This exploit of DC’ing to skip cutscenes represents a choice within the instance, and that’s why it’s a problem that needs to be addressed.

Given that the roulette system exists purely to encourage players to run level synced content to give newbies more players to play with, then it runs at odds with that philosophy to make cutscenes skippable. You’re making the content intended for newbies completely unfriendly for newbies.
If you want to run MSQ without the cutscenes, then it should be you who uses PF or runs it unsynced.
If you want the rewards that have been specifically tailored to a 45 minute long instance, then you eat that time, that’s the price for the high reward.