They aren't the same ones, or are they?
No, they aren't. They are meant to be a Biblical reference just like 99% of the rest of Xenogears. Although, they
may be a subtle nod to Chrono Trigger since Lucca appears in the game as a full cameo. The three are ancient sages of Shevat, and Melchior could roughly be approximated as a "guru of life" in that he has mastered nanotechnology and used it for purposes of genetic engineering. Additionally, Belthesar excels at working with machines - same as in Chrono Trigger. Gaspar...doesn't do much really. He isn't like a "sage of time" like the others are sages of "life" and "reason".
Additionally, all three are sages of Shevat, which is a floating "country" in the sky. Coincidence? Unlikely.