That is why I said this:
It shouldnt be an issue in the long term.
The Moros dont have any significant amount of population to populate Mindanao or Borneo. If Philippines were a British colony and Rizal were alive, the Borneo project migrating Filipinos, Catholics to Borneo would have happened.
The same thing happened with the Americans otl management in Mindanao. They didnt rely on the Moros to populate Mindanao. They relied on the Christian Filipinos.
Regardless, war Spain vs Britain wont happened if there is so much imbalance of power and Philippines already belonging to the British Informal empire especially in the 1890s. You need somewhat parity to have this happen which is why I place the situation Seven years war.
The most important resource is people. And Luzon has more of those. Even up today, Mindanao's natural resources is not optimized, because some people in Mindanao is waiting for someone else to do it rather than doing it themselves.
You can develop without Natural resources but cannot develop without a competent populace.
However, Sulu is culturally and geographically near enough at Malaysia for it to be filled by Malays, hence forming another princely state. However, Zamboanga is too Hispanized to be included at the state.
And who the hell will go to what they see as undeveloped islands? I'll be frank but Luzon and Mindanao are much more economically significant since they have more resources and more logistically viable, due to it's "oneness".
Also, Mindanao is settled by Visayans since Visayas is much nearer on it than Luzon.