World War II, and the disruption to European colonial holdings caused by the period of Japanese invasion and occupation, is generally seen as a key step in the eventual independence of many countries in Southeast Asia. It also seems that while the Japanese might have been just as hated, if not more so in some cases, by the local populations, they nevertheless did strike an important, if not fatal blow, to the image of white, European superiority that the colonial powers tried to cultivate. As far as I know, none of that is too controversial.
But what I'm wondering is how much that disruption and pulling back the curtain played in the actual coalescing of national identity and creation of liberation movements in those regions. That is to say, was there a real sense of Indonesian identity prior to 1942, or a strong liberation movement present in the years before Japanese occupation, and if not, can we tie its rise to the perception in changed power dynamics?
Additionally, did the Japanese military successes, even if not permanent, have any similar influences within colonial possessions outside of the region that they actually operated in, such as Africa?
The 'invincibility of the white man' is a theme that was often brought up by former colonialists who witnessed the Japanese occupation, and who later became academics in the 1950s-60s. For example, Paul Mus and Harry Benda either fled Japanese troops or were interned by them in the Indes and Indochina. I would argue that Japan's military success was much more a shock to their psyche than it was to their Asian counterparts. The far more important aspect is the simple break in colonial authority, which allowed for revolutionaries to seize power. The French empire presents an interesting case, as France lost control over some colonies and kept it over others. The primary factor allowing for the post-WWII revolutions was the absence of colonials, rather than the strength of the nationalist or communist movements.
While you note that 'the Japanese might have been just as hated [as Western colonialists]' this is more Western perception or the influence of post-colonial nationalist histories. At the time, many Southeast Asians looked at Japan with admiration (as they had since ~1904), or at least as a crucial ally that could help them overthrow Western imperialism. Japan was very much seen as a liberator in Indonesia. It was likewise favorably seen in Indochina, initially, but Japan's refusal to similarly grant it independence soured that enthusiasm.
The most significant factor was that the Japanese interregnum allowed local organizations to mobilize their populations in ways that would not have been possible under colonial control. Suharto could not have toured the Indes building support for a national Indonesian state. Nor could have the Avant Garde Youth in Vietnam have organized under the Japanese sponsored Empire of Vietnam government, which later formed much of the Viet Minh's strength. Prior to this, the Indochinese Communist Party (ICP) had planned to organize the entire space of Indochina (today's Vietnam, Laos, and Cambodia). But the Empire of Vietnam, formed in early 1945, was the first state to use the name Vietnam, to unify the country's three regions, and develop a national identity. This prompted the ICP to adopt a national front broken into three (Viet Minh, Pathet Lao, Khmer Issark), though each were dominated by Vietnamese ICP members. Those mobilizations and propaganda campaigns were crucial in building support for their respective post-colonial states.
It wasn't that Japan transformed Southeast Asians, but rather that their victory allowed them to transform themselves. The other main effect is the support that Japanese officers gave to their SE Asian counterparts, lending them important supplies and advice in building their new armies.