I can only go by your summary by Innes-Robbins' arguments since I do not have access to his book right now, but I wouldn't claim that Portuguese strategy was in any way remarkably flawed for its time. In fact, one could argue that it was following a pattern that we see in specifically European counterinsurgency in Africa during the 1950s through the 1970s: Conscripts drawn from the metropole with low morale, often stuck in static and passive duties, while elite formations such as paratroopers were tasked with functioning as offensive formations.

More specifically, Ian F.W. Beckett emphasizes that Portuguese technique was drawn from French and British concepts in Algeria, Indochina, Kenya, and Malaya. Portuguese theoretical works on counterinsurgency drew heavily on past writings in British and French, as well as being influenced by concepts like the French guerre révolutionaire. This is perhaps most visible in the Portugese armed forces official COIN manual, O Exército na Guerra Subversiva (1963). When deploying forces in the fields, therefore, they had theoretically the both of best worlds.

Yet, as many historians dealing with COIN would argue today, this is never enough. There is no 'one-size fits all' model that will guarantee victory. In fact, modern COIN scholarship has moved away from notions of 'ways of war' as being the key to understanding success or failure in COIN conflicts. Local factors are always paramount in deciding how matters will progress. The saying that "no plan survives first contact with the enemy" is very relevant when considering conflicts involving asymmetric warfare.

Take, for example, the fact that Portugal was involved in three conflicts that all overlapped in three different geographical regions on the same continent. The intense need for a build-up of troops practically required giving up the initiative to the insurgents. The platoon-size sweeps that you mention were a reality, and incredibly ineffective. For regular units, the battalion became the basic unit. There was a heavy focus on military over civic matters, the latter being the most important factor to consider when dealing with insurgents. Even when there was a focus on so-called 'hearts and minds' campaigns, they were either underfunded, disastrously carried out (the resettlement strategy, the aldeamentos in Mozambique, comes into mind), or were negatively impacted by the Portuguese military strategy. Even if the conscripted Portuguese forces were divided into squad/sections, trained to some degree of efficiency, and dropped in the bush, it would have meant little if they didn't work within a larger military-civic framework. France's experience in Algeria is perhaps the best example of this.

There are a great many factors that come into play when discussing flawed COIN strategies. I have only scratched the surface when it comes to the Portuguese experience in their African colonies, but it is important not to buy into the idea that the Portuguese COIN efforts were successful, as some older authors would argue, since this usually argues along a 'stabbed-in-the-back' myth that is popular in failed COIN campaigns as well as completely overlook the fact that the civic aspect of the conflict is as important, if not more, than the military aspect. But Portugal was not alone in this. Both France and Great Britain failed in their COIN campaigns in Africa, showing that their theoretical frameworks couldn't guarantee victory even for themselves.