As far as I know, there is no direct or indirect mention of Dalton's role in the present-era other than what was established in CTDS. What I think is that Masato Kato had a good idea what Dalton's role in the world was supposed to be at the time Kato made Chrono Cross, but was unable to implement it in the game due to money and time constraints.
This is purely conjecture, but this is what I believe happened: Dalton takes control of Poore sometime before 1005 and then launches an attack on Guardia Castle. Dalton finds the Masamune sealed in the castle archives (left behind by Glenn in the middle-ages) and uses it to kill Queen Nadia. This action curses the Masamune. Crono, having no idea what has happened, flees with his infant daughter, Leena, during the confusion. By the time that Crono learns of Marle's death, Dalton has already been killed by an enraged Lucca, who uses her powerful magic to obliterate Guardia Castle with Dalton still inside. Lucca's attack causes severe damage to Truce, leaving many children orphaned, and she decides to take the children in as penance for her rash act of vengeance. With Poore in control of Guardia, Crono goes into exile and changes his name, raising Leena in the remote fishing village of Arni in the El-Nido archipelago.
Obviously, the part about Leena isn't canon, but technically neither is anything else. This is what I think the original idea was, and Kato was forced to reject it, only hinting at it years later in CTDS while not contradicting anything that was portrayed in Chrono Cross.