when I duplicate the experiment and clone it remote, the call is ignored and the recorded values are used?

Yes ScantChimpanzee51 exactly.
Think of it as the inital value you want to put on the Task when you are running the code on your machine, later when you clone the Task, you can edit the base docker image in the UI (or with the API), of course the new value is used when the agent spins this Task, and to avoid the actual docker (the one you changed in the UI) to be overwritten by this call (the set_base_docker call), it is essentially skipped over