As I am reading this question, there are thee separate but definitely interconnected issues to discuss here:

1. How did the Portuguese Empire look like in SE Asia
2. What was Portuguese Empire's internal organization and attitude to different parts like Brazil, India, SE Asia etc.
3. Why did Dutch manage to 'win' or succeeded over out Portuguese

To be honest, the comprehensive answer to any one of the three fills a book. But let's try and give a rough overview.

Now Portuguese empire in Asia, called Estado da India was from its inception focused mostly on Western coast of India and the Arabian Sea (western part of the Indian ocean). Here there was their Capital, here they had built the chain of their fortresses controlling the major trade center like Ormuz, Diu, Mozambique, etc and exerted their power over the major spice producing areas: Malabar coast for pepper and Ceylon for cinnamon. In contrast, the SE Asia seems like peripheral importance. The Portuguese contended themselves with just taking Malacca, which wasn't a small thing as it had at the time almost monopoly for through-port of the goods from that region and beyond. With the addition of Macau in China and some smaller (and short lived) presences like in Japan or the one in the spice island of Ternate, that was the only major presence they had in the region. And from Malacca Portuguese never really tried to conquer surrounding areas, which they wouldn't succeed anyway, as they were preoccupied with trying to survive by pitching their neighbors against each other (Sultanate of Aceh and Sultanate of Johor the usual culprits). There were some floating ideas in Portuguese royal court to divide Estado da India to three equal regions, of which SE Asia would be one, which theoretically could lead to more conquests and control in the region. But that idea was always refused by the Governor-generals of Estado on the very real basis that Portuguese forces were already stretched thin and for most times, when Portuguese wanted to conduct a major military operation (be it new conquest or increasing defense of existing forts) they had to exert themselves and round up ships and men from all corners of the Estado - so a division of commands would effectively prevent this united response and doom the area. So the overall command was left in the Governer-General in Goa, who was mostly preoccupied with Indian affairs so there were never enough resources for further increase of presence in Indonesia. More on Portuguese organization

Here we broached the subject of different priorities of the Empire, and as well that of under staffing and limited manpower resources, which your source also touches, although in a very clumsy way. The lack of manpower really was a problem, and it seems that by the end of 16th century Portuguese much preferred emigration to Brazil, then Asia. I recently answered a short question, where I put a quote from The Portuguese empire in Asia, 1500-1700 by Sanjay Subrahmanyam about rising population of Brazil (and Atlantic) contrasted to Asia:

The former of these two points is fairly clearly established by the evidence on the shifting relative population of different parts of the Portuguese overseas empire. By the end of the sixteenth century, the settler population of Brazil was just under double the “white” population of Portuguese Asia, whereas in around 1550, it had been about one fourth the latter. From a total Portuguese emigre population about 1600 of over 100,000, Brazil accounted for a third, Asia for a fifth, and West Africa and the Atlantic islands for the rest

There are several propositions for why this happens. Some propose the allure of agricultural - slavery fueled- living was more to general Portuguese liking then commercial/merchant way of life in Asia. There is also the fact that Asia seemed to be considered more dangerous (wars, hostile local enemy states which were of stronger then ones in Brazil and Africa) and difficult to live in (harsh tropical climate, diseases, monsoon weather), and not to mention the trip there was long and difficult with high mortality. And getting there was expensive, limited to royal ships and only way a common man could afford to go was to enlist for 3-year service - underpaid and difficult. In contrast going to Brazil was closer, cheaper and safer so we shouldn't really wonder why it was more popular. I am not sure how to measure the importance of above reasons, but I am sure they all had their weight. And when the other Europeans started encroaching on Asia, the biggest incentive for Asia - the profits - started disintegrating.

We have now reached the Dutch. I am not an expert on them so forgive me some simplifications. First for the analysis of the demographics of home countries, I would recommend against comparing them solely on population. The Netherlands and Flanders had been since the Middle Ages one of Europe richest, most urbanized, most industrialized regions, major center of manufacturing, commerce and finance. Portugal.... was not. In fact, if you study the Portuguese spice trade of 16th century you will see how heavily interconnected it is with the Low countries, so when Portuguese were getting rich so were the Dutch, and that didn't work the other way. To move to 17th century, and VOC (whose very concept of stock company had advantages vs. Portuguese royal control) arrived to Asia. They unlike the Portuguese, immediately set up their Capital in Indonesia and centered their activities there. This brought another benefit that their routes to and from were mostly independent of the monsoons like in India. From Batavia, the Dutch procured pepper from Sumatra (and later took Malabar from Portuguese in 1660s) and from there were much closer to control the Spice islands and more expensive spices like cloves, nutmeg. And once in they proceeded to kick Portuguese out. It took them some time but slowly but surely they kicked Portuguese from Malacca, Ceylon, Malabar, Elmina etc. They failed to dislodge them from Goa, Mozambique, Macau. But interestingly (parts of) Brazil and Angola were taken by the Dutch for a brief period, but Portuguese pushed them out and retook the areas. This certainly plays into the whole above narrative of Portuguese prioritizing Brazil and their Atlantic empire above SE Asia (or even India) and focusing their limited resources there. More on the failure of the Portuguese at the time

I am not sure how much of the above has sense and how much it answers your question(s). I find it not surprising the Portuguese left no major mark in SE Asia as they had pretty much one holding there (Malacca) which they lost and that anyway dropped out of importance. They had not enough resources (not just manpower, but that as well) to fight on all the fronts against another european opponent, richer at that. And they had at the time other priorities, like Brazil, where their presence was larger and easier to defend