LA Capitan (and by extension La Comadora) is frustrating for me in terms of timeline.
She snuck onto the ship disguised as a boy. To pull that off she would have been… what 10 to 14 years old?
She was effected by the "Void" she fell in, it was in the ocean so maybe an early form of "The Void"? Or but art for the event is on Time Cataclysm, so maybe it is the beginning of the Singularity OblivAeon is creating.
This leads us to "Curse of the Black Spot", the Time Energies effected her, perhaps taking a massive toll on her body perhaps the curse is something else entirely. To cure herself she has a hi-tech compass which seems reminiscent of the compass from Pirates of the Carribean (which pointed to the persons greatest desire). It looks like she's at least 18 but probably older, so it is safe to say this takes place ten years after she gets the ship.
My best guess is that she went to the Nexus of the Void to find a cure for the Black Spot.
After curing herself, or being cured by one of the heroes, we get her in her early piracy career. Perhaps Chiquito is from the Nexus, being the only companion she's had in many years alone. He could have even grabbed a piece of Omnitron-U during the conflict with OblivAeon or the Aeon Men. Correction: Looks like Chiquito appeared in the Final Wasteland on her first trip. This early Captain is defeated and given by Chrono-Ranger to the Elder LA Comodora.
She somehow escapes from her older self, gathers her crew, and becomes the Captain we all know from Shattered Timelines.
After many years and many defeats she abadons her crew, eventually runs into Chrono-Ranger and hires him to go and grab her younger self. Then after securing her younger self she goes and helps fight OblivAeon and save all of time and space.
Alternatively, Black Spot could take place after She is captured and given to the older captain. La Commadora transfers the terrible Black Spot to her younger self, who goes hero while trying to get a cure, then in retalation for how she was treated by herself gathers her crew and becomes the captain we know and despise.