They're different crowns really and while everyone wants to debate which is the more prestige, they represent different things.
The world championships is a one off race. You get one shot, one run and if you make the slightest mistake then that's more or less your chances of securing the title over. Consequently the race favours the rider who can keep the coolest head and is genuinely fast. You could have a world champ because they are so far ahead of everyone else that they can ride at 95% and still beat everyone else (Sam Hill at Rotorua) or you can have a rider who is just supremely good at focusing on that one run, not making any mistakes and dealing with the pressure that comes with the title – Fabien Barrell at Les Gets, where Peaty binned it – sad but that's the worlds and that's the effect of pressure; Gee Atherton in Italy when Sam Hill binned it on the last corner, when he really should have backed off the gas a little and still won by several seconds.
The World Cup on the other had rewards consistency and adaptability; you have to be good over a range of courses, you have to be consistent and you have to be able to adapt your riding style to suit. You can afford to make mistakes, like Sam Hill at Andora where he binned it big time, but still win the overall because you make up for it by winning other races and placing well.
I personally can see that the World Champs may have a little more prestige associated, just because the rainbow stripes have always been so highly regarded in cycling in general, but I think IMO, that the World Cup shows who the best rider really is.