They cannot remove pursuits and such, because you needn't forget that IBU cup is not only a qualification competition, but it is also the gateway for younger, less experienced athletes from larger nations such as Norway, Germany, France etc. that would be sent off to the World Cup level, get a 35th place in the sprint and would have 0 pursuit competition experience compared to athletes that have long been on the tour.
For example, Lithuanians ALWAYS go backwards in every single pursuit that they participate. Why? Mostly because we never qualify to them, so pacing problems, shooting problems, all of that really can be seen in a technical race such as the pursuit. And most especially that's the only HEAD to HEAD practice if you can't qualify to the mass start and in relays, the second leg from smaller nations is usually already out of it, so you're on the shooting range with two other people at best.
Another point is that you can't overcrowd IBU cup with individuals either, because athletes from smaller nations would just die on the course. People lose 7 minutes in the sprint, seeing yourself 22 minutes behind in 104th place would not really inspire you to compete further.