The relationship between the Philippines and the United States is fine. In fact, for the last 50 or 60 years, both countries have had each other's back. Both countries believe in democracy, and agree on many things. Since the Philippines was named independent after WWII, conflicts have not existed between the Philippines and the United States.
Obviously this is a complete change in relationship from a little over a hundred years ago. It turns out, in the end, the United States agreed with Twain; there was no reason to try to imperialize the Philippines. They would be fine on their own and didn't need to be "civilized." Twain would agree that the U.S. should be making friends with other nations and working with them in place of fighting with them.
However, the same cannot be said about the United States and Muslims. After all, the Moros were Muslims, and after being needlessly shot in the Moro Massacre, some of the Muslims could not let that stand.
Around the beginning of the 21st century, some Muslim extremists from the Middle East retaliated by attacking the U.S. like on September 11th. This lead to the U.S. going to war with these Muslim dominated countries in the Middle east. This may be a long term effect of the Moro Massacre.
Some Muslims resort to violence, and some still may not agree with what the Americans did in 1906. But, relationships are much better than they were at the beginning of 1900s. And Mark Twain would like it that way.