It is a feature - not a bug
Nevertheless, we will fix it
You need an automatic layout to allow for collaborative modeling and to allow for quick modeling, e.g. facilitating a workshop. The trick is to change perspectives to get a better look on the overlapping connections. The feature that allows for a temporal change of factor's positions is just for screenshots and presenter-entries.
However, the fact, that the factors are arranged on a horizontal line annoys us, too. Therefore we are currently improving the autolayout significantly. But that is yet a secret