Are you using TreeLayout? It appears that those dots are making the node taller. If layers are aligned on some sort of grid, that might increase the distance between the layers. It would be useful to confirm that this is the case by having a node under the bottom “Position” on the left side branch.
And how are your node and the “PositionsTreeExpander” defined?
So, everything looks good except for the vertical position of the collapsing button, yes? Why is that affected by the presence of the other objects?
I wonder if your node template has gotten too complicated for me to understand, so it would be better to use two separate templates: one simple one and one with all those details. GoJS Template Maps -- Northwoods Software