Maltese falcons were already very famous, in part due to the treatise on falconry written by Frederick II, Holy Roman Empire, among which titles is King of Sicily, at a time when Malta was a fief of the Kingdom of Sicily. So, Maltese falcons had long been very desirable, and given the popularity of falconry among the royals of Europe at the time, to be gifted a Maltese falcon is a sign of honor.

Even today you can order a copy of this book, "The Art of Falconry", although you may have to spell out the author's name as "Frederick Second of Hohenstaufen."

Now, on to the technicalities of history and early modern Spain. The grant was given by Charles V not as King of Spain -- "Spain" didn't exist yet -- but as co-King of Aragon, of which Sicily was a fiefdom, of which Malta was part of. At the time of the grant, Charles V was jointly ruling Aragon with his mother Joanna, even if she was not an active ruler. So the falcon was paid not to the King of Spain, but to the Viceroy of Sicily.

Further, Charles V didn't "give" Malta to the Knights, he rented it to them, under feudal contract. This is why the text of the grant specified what should happen in case of succession of the grand master, who should assign the bishop of Malta (the viceroy of Sicily, not the knights), how Malta should not engage in activities against Sicily, etc.

Perhaps most telling is that there are conditions for returning Malta to Sicily if/when the Knights were able to re-conquer Rhodes their original home, or if it decides itself to relocate elsewhere.