Start with Lesage.
Burt gives him command of the little sloop Windward after depositing Chris on Hispaniola. He's still in command of it when Chris puts into Port Royal after taking the Castillo Blanco. (Both pieces of info come to Chris from two former Windward shipmates, who left the Windward a week before.)
Shortly after this, Lesage is captain of the "three-master" Bretagne. (This piece of info comes from buccaneers on Hispaniola, when Chris drops by there to look for Valentin.)
The narrative doesn't make much of it, but as a "three-master" the Bretagne is surely the largest of the pirate ships. For example, the Weald is the largest of the flotilla Burt leads around the Horn, and she is a two-masted brig. Anybody who knows something about nautical history can correct me here, but I think the Bretagne must actually be a galleon.
How does Lesage in a tiny sloop with a handful of men take a
galleon in the short time available to him?
We have a galleon candidate: the Santa Lucia, which Chris fights on his way from Port Royal to Hispaniola. He leaves her crippled; still too big & dangerous for the Windward by itself, surely, but in conjunction with some other larger ship or flotilla which somehow knows of her plight & position ....
Fast forward to Rio Hato, the site of Lesage's treachery. Recall that Lesage turns up there in the Bretagne with four other ships in company.
Question: how plausible is the picture of Lesage leading a flotilla around the Horn, given his apparent inability to keep a crew together and his unpleasant reputation?
He tells Burt and Chris that he missed them at Portobello, but knowing Burt's ultimate goal, he sailed as fast as could from there, finding them at Rio Hato. Chris says he should have spotted a "big hole" in this story.
I'm not exactly sure what the hole is - we know that Lesage had been told about Portobello and the Pacific plan, so no hole up to that point. But I assume it must have to do with the timing. That is, under reasonable assumptions, if Lesage had sailed swiftly from Portobello, he should have arrived on the Pacific side of Panama long before Burt's flotilla. Between Portobello and Rio Hato, Burt et al had recruited amongst the Cameroons, taken Maracaibo, refitted at Port Royal, spent a long time finding a wind through the passage, spent a few weeks recuperating, waited 10 days off Callao for the treasure fleet to sail, and then chased it north to Panama.
Next question: How does Lesage appear at Rio hato at just the right time to work his treachery?
Obviously, I'm pointing the finger at Ignacio with all of these questions. I think we have the answer here to what he was actually doing since "losing sight" of Chris in Veracruz.
First up - motivation. Burt's stash is far less than the value of the Spanish mule train. To the extent that Ignacio is driven by desire for $$$, he will want to get his hands on the bigger pile. IMO, this is in fact a primary motivation for him. He might want to go sailing around the world with Novia and his kid, but he wants to do it with lots & lots & lots of money - as he imagiens to himself on the night of the treachery. When Fr Chris writes of having "planned every detail", what he means is the plan culminating in this treachery.
(Burt speaks of being able to go back to Surrey and buy a tidy estate when he's added some more to his stash. One tenth of a commander's share of the mule train is enough for that purpose. On the figures Burt gives when he describes the train to Chris, say around $500K for his stash, and $50M-$200M for a mule train, in modern dollars, and acknowledging that such comparisons are always very rough.)
Second - execution. As I wrote before, I think that Ignacio in 2010's-era Cuba has already recovered Burt's stash. He uses proceeds from this to finance the venture, once he's back in the 17th century. Buys a ship, recruits a crew. He knows where & when to find Lesage: at Port Royal, a week before Chris sails for Tortuga, if not before. Meets him, recruits him to the plan (Lesage is also a money-driven kind of guy), gets him to chuck people who already know the young Chris off the Windward.
Go find the crippled Sana Lucia, take it, install Lesage as captain (renamed the Bretagne presumably in honor of Lesage's birth-place) and cats-power flotilla leader. Quite possibly stop off at Hispaniola to get rid of Valentin (though I'm not clear exactly why
- maybe it's a device for getting a better hold on Lesage, who would be prime suspect in any murder investigation ... dunno).
Possibly the two ships are then positioned as a Spanish pirate force, perhaps with a base at Veracruz (Fr Chris explains how Spanish and Franco-British pirates rarely have much to do with each other). Ignacio is the real commander but Lesage fronts - obviously he doesn't want it widely known in Veracruz that he's in charge; this could get him "in the soup" with Novia later on, after Chris has gone back to the future.
Ignacio engineers the Portobello incident by writing the letter which Gosling intercepts, giving time to assemble his own larger flotilla on the one hand, and reducing Burt's manpower on the other.
Follows Burt around the Horn, arrives at Rio Hato at just the right time, do the dirty deed, grab the gold, take the biggest share, meet Chris & Novia in Veracruz with a big grin on his face ...
Although he probably regrets Burt at al's death a little, it's
already happened and God isn't going to punish him for something which happened in his past where he was a victim too (or some such casuistry). He would have given strict instructions that Novia was not to be hurt or raped, but there had to be enough rough-house to avoid suspicion.