I was able to bypass the problem by using the info here: Observe modified segment - #2 by lassoan to create a log of executed effects (I could do that because we have segmentation steps that execute sequentially fixed segmentEditor effects or allow user-interactions like paint effect)
And we decided to only give support to undo/redo the paint steps of our workflow.
However, there is a bug on the segment editor that breaks our custom undo/redo logic.