I am not really knowledgable in the inner workings of the Spanish court or the thought processes of Phillip II and hopefully, some of the others flairs, like u/drylaw, can shed some light from this angle... But I am a bit knowledgeable on trade and navigation of the period, and my contribution will hopefully illuminate some matters here a bit.

It was very much normal for rulers of the period, especially Iberian ones, to grant monopolies or similar exclusive rights to their subjects or groups as rewards for preformed services, or as it was partly the case here, to encourage the development of certain areas and regions. Such was the case with Manila galleons, on which exclusive rights to travel and ship goods were given to residents of the newly established (1565) colony in the Philippines. Of course, the eligible colonists would quite often (technically illegally) resell their cargo space to non-resident merchants that nominally shouldn't have this privilege.. but the point is that the rights of the monopoly rested in the hands of Manila merchants, not Europeans.

The European commercial interests did have their monopoly though. They rallied behind Casa da Contratación which had exclusive rights on granting licences for travel and trade between Europe and Americas and back. And as such enabled desirable merchants (usually based in Seville and Andalusia) to have the hold importing goods and supplies to the growing American colonies, organized in those times in two Viceroyalties: New Spain/Mexico and Terra Firme/Peru. And it is this monopoly on imports to the Americas that was under threat due to imports from Asia. Huge quantity of cheap, predominately Chinese textiles, porcelain and other goods was quick to flood the markets in America and push out the Europeans goods forced on the colonists by lack of other options.

It is in this light we might look at the edict of 1593, which is actually only one in a series of numerous similar edicts trying in one way or another to regulate trade, usually with the intent to limit the trade in favour of European imports. For example, while in 1579 Peru was granted permission to trade directly with Philipinnes, after several successful voyages, the licence was revoked in 1582 and ban of trade between Peru and Asia was reissued with various legislation in years of 1591,1592,1593,1595 and 1599. The regulations didn't stop at just banning the trade between Asia and Americas, as various edicts were issued limiting the trade between the two viceroyalities, e.g. in 1587 Chinese goods were completely banned for being shipped to Peru, then all trade was limited at two ships that could carry mot more than 200,000 ducats worth of goods of exclusively Mexican products, before completely forbidding direct trade between the two viceroyalities in 1604, decree of which specifically mentions excessive increase in trade in Chinese stuff as the reason of the ban. The decree was reissued in 1609, 1620, 1634, 1636 and 1706.

All this shows the serious effort by the Spanish Crown to curtail the amount of Asian goods flowing into Americas because they were perceived as damaging the economy and commerce carried by the European merchants and manufacturers, and limiting the Manila-Acapulco trade can be seen as an extension of these protectionist policies. The maximum being set at two ships seems to be chosen by the existing situation as in 1590 - so before the edict - there were at most two ships making the voyage so that was probably the realistic maximum amount of trade possible at the time. The people in Philipines would have loved there to be more ships, as we see throughout the 17th century when they regularly petitioned the limit to be raised, however, their pleas were unanswered. And so the limit of two ships remained...

(also a final note. my answer mostly focuses on trade decrees and economic interests of certain groups, but I just want to stress out that the period in question - 1590s - was a very precarious time for the Spanish commerce and maritime matters due to the war with the English and the Dutch. Everybody knows of the Armadas of 1588-89, but both the period preceding and following was full with privateering/piracy that incurred heavy losses on the Spanish crown. This included Drake's foray into the Pacific in 1578 and laying bare the vulnerability of the Spanish position there, as well as his 1585 raid of the Spanish Caribbean. And in 1590s English pirates lying in wait near the Azores intercepted several Portuguese and Spanish treasure fleets. All in all, in 1590s the war on seas raged, and the Spanish were very exposed, and security concerns may well have shaped their choices)

Sources:

Mexico, Peru, and the Manila Galleon by Schurz, William Lytle

Trade and navigation between Spain and the Indies in the time of the Hapsburgs by Haring, Clarence Henry