I wonder that as well. To me the promo La Comadora looks to be in between Villians La Capitan and Regular La Capitan.
Reading the description of Chrono Ranger's promo it says "The folks on the ship fixed up his arm and his badge, and the captain of the ship just asked for one simple thing in return: fix the mistakes of her youth. Apparently, she'd made a mess of things when she first got that ship"
So what if the "mess" is not piracy in itself, but getting the Black Spot, she wants Chrono Ranger to stop her younger self from doing whatever she did to get the Black Spot, so Villains La Capitan is pre Black Spot, once Villains La Capitan gets the Black Spot (or avoids it) La Comodora is not so worried about further pirate shenanagins and lets Regular la Capitan continue on. Probably still focusing on a way to stop her past self from ever getting the Black Spot. (though it may be a fixed point and she can't stop it)