BTW, you like Muramasa a lot right? Did you read the sequel manga? It's canon right? Please tell me it's so....a continuation where both Chacha and Hikaru survive. It has to happen
Masada's stuff is quite straightforward in route progression actually. Either there is no order or the game is such that it makes you play the correct order.
It's simply whose POV you get. Example, for Keishiro/Bey's route, you get to see how he trolls Hajun with that wound at the end, while for Yakou you see how he learns the truth behind the Throne system and basically facilitate the counterattack against Hajun.
Any order is fine, just leave Habaki's for last and the grand end will begin after all is done