The principle problem with the situation is that when it came to the Tudor period- such clear lines of demarcation between civilian and military operations simply did not exist. England managed, through the reigns of Henry VIII and his daughter Elizabeth to develop what was arguably the one of best organised fleets but its organisation was unique amidst European nations. Effectively it was run by private interests.

From the earliest incarnation of the ‘Council of the Marine’, the chief officers of the admiralty had been filled by men of proven competence in matters regarding ships. But while they held offices of state and were acting as royal officials, they never ceased to be private shipowners and merchants.

Which allowed for many examples of what we would run screaming from today condemning obvious ‘conflicts of interest’ but for contemporaries were seen as legitimate business opportunities.

The crown simply co-opted their expertise (without which they could not have run a successful fleet) but these private interests gained considerable control over the Kings and Queens ships. They could, and frequently did, charter them for private voyagers. They could, and did, sell navy stores in their personal accounts. They were able to appear both as royal captains, admirals and even Officers of the Admiralty, while also being private merchants, shipowners and if need be, pirates.

Unlike Spain who would co-opt merchant shipping (for example the staggering numbers of merchantmen used in the Armada); this was more an informal partnership, which was, as Rodger’s says ’not of equals but of parties neither of whom could do without the other, and each of who could exploit the arrangement to his own advantage’ (p227).

Naval fleets cost copious amounts of cash; Henry left Mary a perilously poor state having lavished extraordinary sums on the fleet, and it was in the best interests of both Mary and Elizabeth to follow on with much more prudent spending patterns on the fleet, which allowed this unique system remain in place.

It was also, at times, exceptionally profitable. We can mention Sir Francis Drakes circumnavigation of the globe in 1577-80 but we forget what it meant in terms of geopolitics and in terms of cash.

Only one man had previously completed the journey (and Magellan had not survived it), but any contemporary would have said the most probable candidate to match the task would have Spanish or another Portuguese or maybe even a Frenchmen. For an English sailor to do so genuinely sent shock waves across Europe.

Added to that the voyage sent a very clear message to the Spanish- their lightly defended colonies in the Pacific were now vulnerable. The entire focus of Spanish maritime policy had been to transport silver across the Atlantic (something they did with masterful skill). This ability to strike where they had never expected to be struck caused great alarm.

And finally, by all accounts, even allowing for Drake to lowball the profits he returned with, his voyage represented something in the region of a 4,700% return on the investors who had put up the initial £5,000 to equip the voyage. The Queens share alone is assumed to have been around £300,000, which she used to pay off her foreign dept and prudently invest in the newly established Levant Company.

Voyages such as Hawkins first trip to the Caribbean (which while not under crown command or fulfilling any Royal orders) was funded by a body of men including two Lord Mayors of London, again the idea of a sophisticated private system of investment going on behind the scenes.

This is not to say the crown didn’t pay for expeditions or military operations without private investment if need be. The raid upon Cadiz in 1588 is a great example, and a somewhat successful (if badly planned and bad tempered). But such examples were notable as being the exceptions as opposed to the rule.

But on the whole operations against the Spanish during Elizabeth’s regime were a private enterprise. It became more profitable to raid Spanish goods than buy them, and private merchants in London made heady returns. Most of the ventures were not the attention grabbing raids upon the Caribbean colonies, but focused upon the eastern Atlantic.

You saw a gathering of investment and management from successful merchants in London, who would fit out ships to be crewed by a growing body of experienced sailors from Plymouth, and in time London and the other south coast ports, and at every level men, weapons, equipment and expertise were interchangeable with the crowns forces.

It was a heady, unique system, not always successful, but creating the bedrock for later British mercantile power.

Examples like the one you cite were indicative of the ongoing prevailing culture of naval operations in the late Elizabethan era.

Hope that helps.

In terms of books? While afflicted by being produced at the time, the ‘Principle Navigations’ of Richard Hakluyt remain an invaluable resource.

Andrews, K. R. ‘Elizabethan Privateering (ed); Cambridge, 1964) Which is a classic study and ‘Drakes Voyages: A re-assessment if their place in Elizabethan Maritime Expansion’ (London, 1967)

More up to date and much more relevant to the study you cite, Luis Santos ‘The English Armada: The Greatest Naval Disaster in English History’ (Bloomsbury; 2018)

N.A.M Rodger ‘The Safeguard of the Sea:,A naval history of Britain 660-1649’ (HarperCollins; 1997)