It takes place when you want it to.
Technically, it should take place before the end of the Reign, because Baba yaga takes all the queen's daughters with her when it's time for a change.
The module could be about chasing down one of those daughters who is fleeing her fate and attempting to garner power for herself. It could likewise be the daughter sent to grab additional power against Baba Yaga by the queen while the Reign is progressing, and gets caught up in it.
Either works. Just adjust the fluff surrounding the module as you see fit...it fits in easily regardless.
The main problem, of course, is that you need to return to Golarion to do the Legacy, and that happens after the end of the 6th book. Setting it post-6th isn't hard at all, you're just tracking down one of the primary threats to the new queen who will probably be making a stab for the throne if she gets control of a power to control a demon lord...
==Aelryinth
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My husband DMs our Archmage campaign, which is high level mages. We started with The Witchwar Legacy, and then segued into Reign of Winter. He trimmed out a lot of the early stuff, and has obviously heavily modified encounters to challenge us. I do think it made a nice start to Reign of Winter, but playing at low levels, you'd need to really alter the encounters.
Otherwise, Aelryinth makes a nice point about setting it as a wrap-up to RoW.