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What is the proper way to handle Timestamping differences like this? How can I efficiently work on the data, just like it is from a real-world, live robot?

I would say configuring rosbag to publish the clock (ie: adding --clock to your rosbag play command line), and set use_sim_time to true before starting your nodes.

If you then only make use of ros::Time, things should "just work".

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