If the Spotlight is to control a laptop/PC connected via HDMI, yes (but then the Spotlight does not have to be compatible with the Flip).
Nothing can be aligned directly on the Flip with the Spotlight (just tested).

Logitec Spotlight works like the mouse pointer, it simply does not draw an arrow, but the ring or circular area over the screen content. This happens before the screen content is sent to the internal or external display. I think - that Spotlight works independently of the connected screen.