The boarding fight is tough but not unwinnable. Tactical hint: you can climb up the cannon barrel at the front of your boarding deck, get onto the enemy deck behind the soldiers, then start hacking them down one at a time. Also, you go to Port Royale to recruit a full crew before you return to Cuba to take the ship. While you're in Port Royale, visit the dungeon. You get some melee practice and there's a nice sword to be found. The dungeon denizens might also have some swords which you can give to your officers.
There are two timers for the Siroco. The first starts when you either get the letter from the commandant or talk to the captain; that is when the ship first sets sail. After that, a second timer starts; when that expires, the ship has arrived safely in port and you have missed your chance to take her.
The choice of ship type is due to mod history. The ship had to be tier 6 or 7 so as not to be too tough for you to take, and also not too much of a free gift this early in the story. It had to be a merchant type as it's a transport, but also a war type as it carries a load of security troops - so, a dual-purpose ship, sometimes described as "versatile". At the time when I was writing this part of the story, a team of modders had just finished the "Castell Friedrichsburg" brigantines and I got the job of creating the interface pictures for them. When I did, I took a look at the ship's stats - tier 6, dual-purpose, available in "Golden Age of Piracy" period. Here was a new ship model looking for some action to bring it to players' attention, and there was me looking for exactly this sort of ship for the story. The Siroco immediately became the Spanish version of the "Castell Friedrichsburg". The whole point of making the ship at Santiago a slightly inferior tier 6 brig was to encourage the player to switch to this new ship rather than abandon and sink her.
Giving the Siroco a broadside or two of grape to weaken the crew is a good idea. Dismasting her is not a good idea, partly because you can't count on doing it before she or the fort does the same to you, and partly because you're going to want the ship in good condition to run away from the fort.
As to why you pick the beach next to the fort: consider what happens when you sail from Havana. You can either turn west, round the north point, and down the south side of Cuba; or you can turn east, down the north side of Cuba, then round the south point into Santiago. Ardent has no idea which way the Siroco will go - picking a beach further up the coast, away from the fort, runs the risk of being on the wrong side of the island and missing the ship entirely.