I thought that the IDW comics didn't fit into the novel continuity. If the Alien Spotlight comics shed light on this continuity and even fit into it, why doesn't Countdown?
Because IDW's comics do not represent a single continuity. Some of them contradict each other; for instance, D. C. Fontana's Year Four: The Enterprise Experiment
and John Byrne's Romulans
miniseries present contradictory depictions of elements of the late 5-year-mission era. So it has to be treated case-by-case. Some of the Alien Spotlight
comics fit the novel continuity or have been referenced by it, but a few conflict with it.