Let’s say you are designing a font in 1000 UPM.
Scale to UPM changes the resolution of units. If you scale it to 2000, the outline that was 1000 before scaling becomes 2000, and the visual size at given font size stays the same. If you scale UPM to whatever value in instance, it will look of the same size, only different in outline quality (try scaling to 50 to see what I mean).
UnitPerEm does not change your outline or metrics. If you simply change UPM to 2000, that 1000 unit outline stays 1000 unit, effectively reducing its size to half. And after export, your font will look half as big.