Maybe. Or TR doesn't mediate the Russo-Japanese war? Or the treaty is more favorable to Russia, making Japan more hostile
No mediation might also mean no end of the war, or at least not as quickly. While the IJN did very well, the IJA took an enormous number of casualties, and Japan was about to start scraping the bottom of the manpower barrel, and economic difficulties were about to set in too. Russia was distracted by the 1905 revolution, but still had enormous resources to call upon, and was starting to get its shit together militarily. All that means is that the RJW wont end as favorably to Japan. That gives two possible points of divergence, either they become bellicose and expansionist earlier, or they are incapable of further expansion. I'm thinking they will be unable to become expansionist, as they are too busy trying to keep Russia at bay. Either way, its at least a generation before Japan can recover enough to try and move outwardly.
I'd have to think a lot more on what a Russian victory in the RJW would mean before commenting on that line of thought.
Anyway you slice it though, the PI will be a weak, vulnerable nation at risk of colonization when the US pulls out. And the US WILL pull out, regardless of what the PI wants. How long they can stay independent I just don't know, some sort of international agreement sort of like what Belgium had might work. This all brings me back to my original position however, I think there are too many obstacles to overcome for this to be plausible.