The dynamic alliance stuff plays into the late game content but there's no super different endings to chase here. When you're getting close to finishing the main story, make sure you've knocked out both naoe and yasuke's personal quests first, since those unlock their final story beats and you'll want those wrapped up. For the full epilogue content definitely take care of junjiro's questline especially soup for sorin and the pilgrimage, those are pretty crucial. Any allies you've picked up like gennojo or yaya show up in the hideout during the finale which is a nice touch but doesn't change the big picture storyline.

The timing on some of this content can be tricky since the seasons affect when certain npcs are available - winter especially can mess with quest timing since people move around less. Something to keep in mind is that if you mess up stealth and get spotted, those guardian samurai patrols will keep the heat on until the season changes, so plan accordingly. When you're making dialogue choices with characters like naoe you can lean ruthless or empathetic but it just tweaks the conversations, doesn't branch the story in major ways.

For the actual ending sequence, you'll get a nice sunset scene with your allies before rolling into those post-credits missions like the pilgrimage, leaving a mark, and out of the shadows. There's some hints about future content with hattori hanzo and naoe's mother too, but that's more setup than actual story branches. The key thing is focusing on completing those personal quests and ally missions to see all the epilogue content, even though the core ending stays pretty much the same for everyone.