I'm not sure what you mean by two of the 3 in Europe, there aren't 3 GP events in Europe and the last time anyone did 3 GPs was IIRC in 2011, when some skaters were eligible for an extra assignment if they wanted it. Carolina Kostner went to Skate America, CoC and TEB.
So I think allezfred was right that it's not just the travel that affects skaters' decision re whether to go to competitions.
I forgot that there was no event in Germany anymore.

So there are 2 in Europe, 2 in NA and 2 in Asia. We definitely see NA skaters do SkAm and SCI and Asian skaters do NHK and CoC. We also see skaters who train in NA doing one of SkAM and SCI and then one in/closer to their home country. Assigning a skater who trains in Canada but skates for France to do CoC and CoR isn't going to happen if that skater and/or their coach has any pull at all (or they want it that way).
The higher a skater is in the rankings and the more popular they are, the more choice they have. Technically it's all on the NGB to invite them but the NGBs do horse trade and they also do consult with the skaters with clout. They also do things like try to invite skaters with the same coach to the same events, if they can. This is why the TBA at SkAm is often either someone skating in the area they are held (when they were held in SoCal, Caroline Zhang got invited even though her results in prior years might not suggest she'd get that invite) or someone whose coach is already there for another entrant.
If P/C went to CoC/NHK it's because they wanted to IMO. They probably feel obligated to do the one in France so "want" isn't the right word for that one. But if they absolutely didn't want to, they wouldn't. They are World Champions and Olympic Medalists!
Now I know someone is going to respond to this with every instance where a coach had their skaters split across events or a skater had to go to inconvenient events. That doesn't mean these negotiations don't go on and it doesn't mean that these factors aren't considered. It just means that sometimes it doesn't work out perfectly for everyone.
I haven’t seen any instance where skipping Four Continents damaged a small fed skater’s reputation or momentum. And that does happen.
It definitely happens only it's often an issue of money for those skaters as they aren't getting a lot of monetary support. They can afford to go to Worlds or 4CCs, not both, for example. Obviously, they will go to Worlds unless there is some compelling reason to go to 4CCs instead.
Nathan doesn't count, because he also arranges his GPs around school. 4CC isn't the only event he skips.
Of course, it counts. All skaters who skip events they are invited to/eligible for have their reasons. Nathan's reasons are school. But he doesn't skip Worlds no matter what his school schedule is.