Seats, in general, have different heights. So the point of contact and rail distance changes in different saddles.
If you get a saddle with a narrower seat to rail distance (as yours) that's when you get this problem.
You can 100% cut or replace the bolt and it will not affect safety. (As long as you don't cut it too short, ie the bolt should be long enough to use all of the saddle clamp nut threads.)
Before you do decide to cut though, make sure you are 100% happy with the saddle position. If you cut the bolt to short and decide to change the position, you can compromise the saddle by not leaving enough threads for to grip properly.
If you should to cut, make sure you don't damage the bolt threads as it could lead to damaging the saddle nut threads.