It's retarded. No one aside from the Duke has any leverage. Miyabi doesn't have to give them any stake. They should get on their knees and beg him to let them contribute before talking about rights. But no the protagonist always has to be a spineless shoelacer bugman.
Ah, yes. The major guilds that have posts in the city have no leverage... Wow. The merchant guild that cares about and controls the trade lines clearly wouldn't send goons after a guy trying to straight up bypass their main service. The production guild sure wouldn't notice all the workers needed going off to do a job that doesn't exist. "Why give them a stake!?" because they are the government who controls the very ability to accomplish what he wants
Sir, it's like trying to build a subway line between your house and your school, illegally. In fact, it would be literally that! Can you imagine what would happen if the town you lived in found out you had built one? Would no one care? Hell no! They would care a whole lot about not only interacting with people's property but about the fact you are trying to create a service without proper permits. On our world, that's jail time. There... it might be execution.
So our main character could build it in secret, under threat of violence and death, only to be used by him and his friend. OR he could get the actual resources to build it, approval of the guilds, and make money. Miyabi is a crafter first and foremost, he isn't great with the politics and isn't a fighter. I see no reason why he wouldn't be shy and feel intimidated by people who have way more power than him. The fact the HE has any stake is impressive because he is such a great crafter. Don't get the concepts mixed around.
Bro, you've got a powertrip MC mindset, not a realistic one.