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"and then a 3D line from there to the 3D sphere. " No, this line segment is also a 2D line. Actually its two lines of different colors, thickness and transparency which gives the illusion of 3D shading. I have a manager which reacts to any camera position/rotation changes by computing a transform of the 3D position of the sphere to a 2D point. The line segment's start x and y are bound to that 2D point. An example of how to do that same dynamic transform but with labels is in FXyz3d: https://github.com/FXyz/FXyz/blob/master/FXyz-Samples/src/main/java/org/fxyz3d/samples/utilities/FloatingLabels.java
"Was this done for UI reasons or mainly to decouple the rendering?" They are decoupled ... mostly... haha. The animated callout is a modified version from the one by Carl Dea: https://github.com/carldea/callouts/tree/master I say mostly because in order to get all these things to work so smoothly and at speed and scale I have had to commit a few "sins" ;-)
That is an overlay extended from LitFX, with the original design contributed by Carl Dea (who is just phenomenal btw) and then I tweaked its colorations, have minimize/close buttons, iconified actions and gave it a useless but awesome fly in animation effect. https://github.com/Birdasaur/LitFX/tree/master/litfx-controls/src/main/java/lit/litfx/controls/covalent