It makes sense that there must be some sort of restriction as to where you can locate a stopover, but I doubt that this is stated anywhere...
Maybe it's something like "if you try and do JFK-LIM-JFK with a stopover in EZE, then you'd need to price it as doing JFK-EZE-JFK with a stopover in LIM, as that would cost more kms".

I think that something strange is going on with the value in km of segments that need connections. This says that JFK-GIG should still be starting at 24k, but the website is just not pricing it like that.