To start with your last point, you are absolutely right, it's a scenario that does not get the attention it deserves: a stuck intermediate flap over a destination with a very short runway can lead to an interesting scenario where you have less fuel than ideal to divert to a longer runway. This is definitely something to keep in the back of your mind, but I don't think you can make hard and fast rules for this (very selective) scenario. Captain A might reason that contingency fuel and final reserve will cover the alternate fuel shortfall in this scenario, captain B would take some extra fuel for 'stuff like this', captain C is far more worried wether the giros grill is still open by the time you make it back, captain D takes 500kg extra regardless, even to Copenhagen. I don't think you will ever get a definitive answer to this question, the important thing I think is that you have considered it!
Now to the typical NEO CNR jitters: this is pure psychology! And I get it. Having flown CEO's for decades, suddenly this hyper efficient NEO flight plan shows up with a CNR which would have instantly caused a fuel mayday call in the past. It takes time to adjust your comfort zone
Personally, flying short haul over Europe, arriving with CNR in the tanks (or slightly below) does not bother me on a normal day, there are plenty of options. If things don't go according to plan, like Morgan wrote before, follow the procedure, call minimum fuel or mayday as needed and make a safe landing.