I think I do understand. Whenever the player's cursor stack changes, driving state changes, or selected entity changes, the mod deletes all path renders and recreates the correct ones based on the current player state (it draws paths for any spidertron that is connected to a remote in your hand, that you are driving, that you have a GUI open, or you are selecting).
This isn't super efficient, but I've never had any performance problems with it before. Even with 60 waypoints, it is only causing spikes of 5ms (which is much less than 1 frame / 16ms). My only guess is that you have another mod which listens to on_chart_tag_added
and does some expensive processing there.
Can you send a screenshot after the freeze, with debug options show-time-usage and hide-mod-gui enabled please?