If I recall correctly, the mod's storyline can be started at any point past a handful of quests from the main quest, if that many. Beyond it, it is pretty much up to the player to get things started when they deem it appropriate. Once in Apotheosis proper, the player will be able to return to Skyrim fairly early, and there is apparently plenty of content in the mod for one to spend so much time there they will be a powerful adventurer when they return even if they did little in the main game beforehand. Bosses level with you up to level 200 and have unique powers/weapons/abilities, so it should remain fairly challenging for a long time (depending on what other mods you use, of course).
In other words, whenever you want is probably fine. Personally I will go through the mod after I deal with Alduin, but before I finish up the DLCs, if only because it'd be cool fighting Harkon and Miraak as a goddess. XD
ShadeTheSilent
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