I did leave spot removal for last step before export JPGs in LR.
However, when I need to re-tune a sequence, I have to redo all spot removal again.

Is it possible not to change spot removal of each picture during a normal workflow of LRT? (I suppose it changes when Read Metadata)

The thing is, that when you apply the transition, LRT will take the spot removal from the first image to all others since it cannot know, that you did individual adjustments. LRTimelapse is designed to support key frame based edits, not single frame edits.
So leave the spot removal for the very last step, when you are sure that you don't have to do any keyframe based adjustments anymore, or do it pixel based, on the LRT_ intermediary files in photoshop.