I think not having Tondo sacked by Bruneians would benefit Luzon in the long term - and why it is because the nobility in Luzon were replaced by Bruneians and the original nobility and the dynasty were either marginalized or fled to the mountains, the Bruneian Nobility in Luzon became the Principalia there in the Spanish times and even supported the Spanish - the only way to prevent that is to make Tondo convert to islam voluntarily.
Since the Kingdom of Tondo is the 'Yamato' state in Luzon, it already have control over the other states in Luzon like Yamato does in Japan and having Tondo not sacked by the Bruneians and Luzon voluntarily islamized would mean the nobility in Luzon would think of them as one with the people of the Island and would think of the welfare of the people like in Mindanao and because of that the Spanish would only conquer a part of Luzon like Mindanao and because both Mindanao and Luzon are mostly unconquerable, the Spanish would have a difficulty in holding what they already have in the Philippines.
I think this scenario is a better scenario for the Philippines since the people in luzon were more enthusiastic about having a nation which conflicts the other part of the archipelago.