When you put a pot of food on the fire before Shabbos, the cooking process begins before Shabbos, and we view the rest as taking place on its own.
Rav Moshe views setting it up on a timer not as if the process already, but as setting it up so that the process will begin on Shabbos.
If you tell a non Jew before Shabbos that you want him to do melacha on Shabbos, unless you later tell him not to, the melacha will be done, yet we don’t view it as if you set the process in motion before Shabbos, we view it as being started on Shabbos.
Rav Moshe considers a timer to be in the same category.