Yes! This exact thing happened between 1580-1640.

King Sebastian I of Portugal led his army, which included a fair portion of the nobility, on a campaign against the Sultan of Morocco. The Portuguese force was heavily outnumbered at the Battle of Alcácer-Quibir in 1578, where they were soundly defeated. The body of the young (24 years old) king was never found, which later led to a belief called 'Sebastianism'- that the brave young king would someday return to save Portugal. Several pretenders claiming to be Sebastian showed up in the next few decades but none had much success.

Sebastian had no children, so the crown passed to his great uncle Henry, then an aged Cardinal who had spent his entire life not fathering heirs. In his last two years of life which he spent very unexpectedly as a monarch, he continued that streak.

After King Henry's death, there were no other close claimants to the throne of Portugal, and Philip II of Spain saw a golden opportunity. He was Sebastian's uncle (Sebastian was the son of Philip's sister, Joanna) and had more or less as good a claim as anyone. Antonio, Prior of Crato, and Duchess Catherine of Braganza had competing claims, but Antonio was a bastard son of a prince (otherwise he would have been the clear heir) and Catherine was a woman (and Portugal had never had a queen regnant) But more importantly, Philip II had a bigger army. He sent the Duke of Alba into Portugal, who defeated Antonio at the Battle of Alcântara (1580) and then seized Lisbon.

The Portuguese Cortes (the governing body) reluctantly agreed to crown Philip under the condition that the Portuguese overseas empire remained under their own authority rather than being subsumed into the Spanish imperial administration. Portugal thus took a position much like that held by Aragon- although both were ruled by the Castilian Habsburg monarchs their governing bodies each maintained many rights and privileges from before political unification. So between 1580-1640, the entire peninsula was united under the Iberian Union.

During the period of union, the Habsburg kings (Philip II, III, and IV) were embroiled in the Eighty Years War with the Dutch, as well as plenty of other conflicts. This put a strain particularly on Castile, over which the monarchs had the most control and which could be more heavily taxed. The Count-Duke of Olivares, chief minister and favorite of Philip IV, had the idea of a Union of Arms between the distinct kingdoms of his liege. Although Aragon and Portugal and the rest contributed to military expenditures, their contribution was far lower than Castile's, and the Count-Duke desired that each polity pay its fair share for the common defense (or offense).

Needless to say, Aragon and Portugal did not like this idea at all, and both rebelled in 1640. While Aragon was eventually brought back into the fold, Portugal won her independence and has remained independent ever since.

So does it make strategic sense? Sure it did, for Castile, because Castile would be the dominant partner. But aside from the use of the Spanish fleet to recover Bahia in Brazil from the Dutch in 1625, Portugal didn't really gain much from the Union.

There seems to be always some confusion on the nature of the Crown of Aragon.

The Crown of Aragon was a federation (or one may even say, confederation) of different polities which included the Kingdom of Valencia, the Kingdom of Mallorca, the Principality of Catalonia, and yes, the Kingdom of Aragon, among others.

But despite the name of the Crown, the richest, most populated, and strongest of its parts, especially on the first few centuries was Catalonia, for obvious reasons. To begin with, Ramiro, the last King of Aragon, gave its Kingdom as a dowry to the Count of Barcelona, Ramon Berenguer IV, therefore the reigning dynasty of the resultant alliance, the Crown of Aragon was the House of Barcelona, which directed its main conquests, was Catalan, as were most of the colonist that went to occuppy Valencia and Mallorca. Also the seat of the government, the Chancillery (although there was no capital per se, the court was wherever the king happened to be) was in Barcelona, which to this day houses the Archive of the Crown of Aragon, one of the biggest medieval document repositary after the Vatican Archives.

So no, "Aragon" did not "control" parts of Catalonia. In the Crown of Aragon no Aragonese laws applied to Catalonia, and no Catalan laws applied to the aragonese, they remained different countries, with different administrations, etc. And the same would happen later when the Crown of Aragon entered into a Dynastic Union with Castille in 1469. Is it true that there were attempts at centralisation by Castille, but they led to serious wars, as in 1640 (which prompted Catalonia to declare its First Republic).