If I have a point on a longitude of 100 W and a latitude of 40 N, how can I backtrack its position or compute where it was 1 mya?
You can digitise a point feature, then give it the plate ID of your rotation, then change the time slider to 1Ma and then click on the feature and you can see the reconstructed coordinates (see screenshot below). Have a look at tutorial 1.5 for creating features.
Alternatively, you can use GPlates web service
See the reference Reconstruct · GPlates/gplates_web_service_doc Wiki · GitHub
Or pygplates if you know Python