For overcoming that i think the collapsing code will have to detect & treat
the loop as single entity. Such that when a loop gets created all
(+-)collapse points on the loop's path disappear. And when a loop is broken
(+-)collapse points reappear.
But, it seems main hurdle here is that the links are not separate objects.
Right now, to include diagrams i use the inline image feature. But, that
causes a lot of to and fro between Freeplane & Diagramming software.
In its current state, to add a flowchart feature, most feasible approach
would be to add a draw toolbar which allows to create/edit diagrams inside a
Node.