I don't have that much of a problem with some 'crazy time travel stuff' being the cause of Jon's existence. There's no way we were ever getting 'Jon growing up in real-time'. For that matter, there isn't really THAT much of a difference between how Clark got Jon and how Bruce got Damian. Even Damian was introduced via a retcon as Batman's long-lost son and honestly, at one point, they did have to come up with some complicated accelerated ageing explanation for why he's the age he is (dunno how that stands currently though). Jon is just the Superman equivalent of that.
Jon being Clark and Lois' son born when they were trapped outside time is essentially the Superman version of Damian being Bruce and Talia's son genetically engineered from a fetus conceived during a night they spent together years ago (which may or may not have involved Talia raping Bruce somehow).