Well, the core of it less of a historical reason and more a linguistic one: Bahasa Malaysia and Bahasa Indonesia are the standardized versions of the same language, spoken Malay. Tagalog and Cebuano, on the other hand, are two wholly different languages. It's a bit like asking why standard American English and standard British English are so similar compared to spoken Irish Gaelic and Welsh.

But why did Malaysia and Indonesia both choose the same language to standardize and use as their national languages? For Malaysia, that's easy to answer: the country was and is driven by a sense of Malay nationalism called Ketuanan Melayu, seeing the Malay bumiputra population as the indigenous rulers of the land. Making the Malay language the national one is just part of enforcing that ethnic privilege.

But the situation was the exact opposite in Indonesia. Ethnic Malays were and are not the plurality group in Indonesia, nor did they dominate economically or politically -- that privilege goes to the Javanese instead. But spoken varieties of Malay in fact has a very long history as a lingua franca of the whole archipelago, from Malaysia to Indonesia and even the Philippines (one contemporary of Cebuano ruler Rajah Humabon famously described his reign as "Kata-katanya adalah raya cita-cita", a sentence quite intelligible to speakers of Malaysian or Indonesian). So even if only 5% of Indonesia's population spoke Malay natively at time of independence, it was still a language relatively widespread as a bahasa pasar (market language) throughout the archipelago. This made the Malay language useful as a national language in an extremely ethnically and linguistically diverse country like Indonesia, and one that could ill afford to antagonize its non-Javanese population where ethnic Javanese often already dominated other arenas.

Quoting Ki Hajar Dewantara of the 1938 Congress of Indonesian Language:

"What is named as 'Indonesian language' is a true Malay language derived from 'Riau Malay' but which had been added, modified or subscribed according to the requirements of the new age and nature, until it was then used easily by people across Indonesia; the renewal of Malay language until it became Indonesian it had to be done by the experts of the new nature, the national nature of Indonesia."

There is a nuance here that you might've picked up: Malay is not actually one single language. It's a dialect continuum that can vary greatly from place to place. Just in Peninsular Malaysia alone, each state has their own variety of Malay and city folk from Kuala Lumpur might not necessarily be able to understand the variety of Malay that is spoken in Kelantan. The difference becomes even larger when you compare it to Acehnese Malay, Minangkabau Malay, Banjarese Malay, and so on. So while Bahasa Malaysia and Indonesia are pretty similar, because they are both derived from the Johor-Riau variant of Malay that was popular among elites due to the prestige of Melaka and Johor, there is a lot more variation in terms of spoken language.

As for Cebuano and Tagalog, meanwhile, they're just different languages outright. Filipino aside, they are not as common outside of their respective ethnic groups, and do not have history as lingua francas before colonialism (instead, traders commonly used Malay variants). Hopefully someone more familiar than me with the Philippines can chime in though!

Sources: Nurdjan, Sukirman; Firman, Mirnawati (2016). Indonesian language for Higher Education

Abdul Rashid, Melebek; Amat Juhari, Moain (2006), Sejarah Bahasa Melayu