Why is the story forcing you to attack French ships when your "served nation" isn't actually hostile to France?
I'm sure there was a reason; I just can't remember now....
Plot. The first one is when you're working for the port admiral of Antigua, doing some jobs for him so that he'll trust you enough to assign you as escort to a supply ship to Isla Mona. (Which reminds me. There's another French ship you need to sink/capture for the port admiral.) As for
La Couronne, that's a bit more complicated. Earlier in the story you find out that France has allied with Portugal, which is hostile to Spain. Taking
La Couronne, which is France's most powerful ship in the Caribbean, is the vice-admiral's way of making the French think that maybe this was a mistake.
Anyway, it is easy enough to mark those particular ships so that they don't cause any adverse nation relations.
That is the same as the solution I applied to the Standard Storyline now.
Except that
La Couronne is not alone, it has two escorts. They'll need to be marked as well.
So, if I interpret "quests_reaction.c" and the contents of "PROGRAM\Storyline\Assassin\characters\init" correctly, you'll need to do this for:
Belleville, captain Rabel Chardon, to be found in "TempQuest.c" (first job for Antigua port admiral);
La Precieuse, captain Clement Bossicar, also in "TempQuest.c" (your second job for Antigua port admiral is to accompany an attempt to colonise Cozumel, but you find the French got there first and this ship meets you on the way out);
La Couronne, captain French_Captain1, to be found in "TempQuestEnemy.c" (his real name is Gilles Chenault but his ID is "French_Captain1");
La Licorne, captain French_Captain2, also in "TempQuestEnemy.c" (real name Aimery Bourgouin, escort for
La Couronne);
Le Foudrayant, captain French_Captain3, also in "TempQuestEnemy.c" (real name Guibert d'Aigreville, escort for
La Couronne)
I'm more concerned with the points where you have to "free play" to make money.
In those cases, I think you do need some sort of legal basis for attacking ships of certain nations.
Surely when the vice-admiral tells you "I want you increase your skills at sea by attacking hostile ships", he doesn't mean "only pirates" or "I want you to ignore what I'm saying here and make some money through honest trading".

So a LoM might be in orer there. Or my proposed "Agent License" to have something inbetween LoM and not having any legal reason for any attacks.
That depends on whether
@Bartolomeu o Portugues wants the player to earn promotions as an intentional consequence of the story.