Well, case in point, the Portuguese rulers never (for 16th century at least) actually styled themselves emperors. Their title was e.g.:

Dom João (III), by the grace of God, King of Portugal, of the Algarves, of either side of the sea in Africa, Lord of Guinea, & of the Conquest, Navigation, & Commerce of Ethiopia, Arabia, Persia, & India

Also, the Portuguese possessions in India were referred to as Estado da Índia translating to something like State of India.

Portuguese 'empire' went through various major or minor changes throughout history, and if one would compare it to the British later one, one would find many structural, political, economical, organizational differences, maybe we can even say philosophical.

That all being said, I really don't find any real reason to not call it an Empire. Sure, if you insist on some rigorous extra pedantic arbitrary rules for what is an Empire modeled only after the British one, it might not fit all your checkboxes. But overall, I don't see a better name for it. It was a monarchical state with oversees territories, that no matter how small, were military, economically and politically under control of the King of Portugal. Also lot of the perceived differences to the British empire stem only because of the difference in territories and time period (height of Portuguese is 16th century, British in 19th) and some I think hold neither true for Britain or Portugal.

Rather then get into a debate of semantics what is or isn't an Empire, i will rather address your points. So:

A highly decentralised bureaucracy to a point where fortress captains etc. are effectively independent from the Portuguese Crown

I am not sure at all why you think the fortress captains are effectively independent. They were appointed by the royal authority (Governor-General, or the King directly) for limited terms. Fortresses themselves were manned by soldiers whose wages were paid for by the royal treasury. The same goes for the cost of the fort and weapons in it. From fortresses money raised from taxes and custom dues would be sent to central authority. While for the most of Estado da India the satellite forts would be connected to Goa, and not directly Lisbon, Goa was directly subjected to the King. Governor-General of the whole Estado da India in Goa would be appointed by royal decree for period of 3 years, after which he would be replaced (in fact, Portuguese kings were highly paranoid that Viceroy would renegade from their rule which is why they insisted on short terms). There was constant correspondence between King and Goa (even though the distance made it highly ineffective). Mainland Portugal would also keep funneling funds, soldiers, weapons, material to Goa, even long after there were shipyards and weapons manufacturing established in Goa.

Sure the individual captains would handle day to day affairs by themselves, and there were (plenty) cases it was directly opposite of central orders, sometimes out of pure corruption but sometimes due to the central authority not being aware of situation and giving conflicting or unenforceable orders (most common was order to blockade trade for military reasons, while at the same time expect the fort to generate profit and feed itself. Those two were incompatible). Basically you couldn't micro manage forts from distance. This brings me to your second point:

Huge numbers of unofficial Portuguese settlements and Portuguese people working against the interests of the Crown

Well, the unoffical Portuguese settlements aren't counted as part of the Portuguese empire, and there were plenty of official ones. And if you think British people (or any other people) were always working for the interest of the Crown, you don't really have a clear picture on how People work. In the end, Portuguese in India were not exclusively agents of the King but free people that could pursue their own interests and paths. They did have a duty to respond in times of military need which they did, so the accusation of them not supporting the Crown isn't really true. And anyway while we can discuss if Portuguese were more or less corrupt then e.g. the british, I don't see how it actually factors in whether we consider Portugese empire or not

Major privatisation, e.g. of "royal" monopolies, fortresses, trading ships

Royal monopolies were Portuguese introduction, used extensively. While at times they 'leased' them to individuals and with time eventually ended them, those were attempts to modernize and create a better economical model as the old one was deemed not quite working. Sometimes the change was for the better, sometimes not. The case is even clearer for ships. After first few expeditions to India participation of private ships was outright prohibited, and only Royal owned ships could go to and from Asia, so I am not sure what you think by mentioning them. In Asia those ships would remain royal property but given to captains with orders where to go and what to do, but in them captains had considerable freedom to trade, which eventually evolved to occasionally leasing ships to individuals and selling older and obsolete ships. Finally, I am not aware what you mean by privatization of fortresses, as I am not aware of such cases, especially major ones

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In the end, nobody really cares much for what name you use. If you insist that it does not conform to your semantics of empire, feel free to call it by some other name. I do feel your analysis of the Portuguese empire is wrong though. For the rest of us, the Empire tag describes the state best it can, and I honestly can't see a reason not to call it that, nor could I imagine a better descriptor. It was an entity which spread from Europe and by military means conquered territories oversees and placed them under their direct legal and political supervision. While distances involved pretty much mandated some degree of autonomy of local capatains, they were clearly integrated into the state hierarchy and bidirectionally connected to it.