From what I have read the long time, the people in Luzon where Katipunan rules don't like Aguinaldo which is one of the reasons the public supported the Americans, what if the Americans decided to oust Aguinaldo and replace him with one of his enemies which have the support of the people, the Philippines would not be united and the First Republic of the Philippines will be renamed back to the Tagalog republic overnight.
In this case Visayas and Mindanao will not be under the the same country as First Republic of the Philippines or the Tagalog Republic since they have their own revolutionary republics, if the treaty of Paris still happens in this scenario how would America treat the Visayas and Mindanao revolutionary republics as well as the Sultanates.