The Tonka version is the most accessible, with the Sega version being released later in its life and in smaller quantities. When Sega seized the manufacturing rights from Tonka in the late eighties, they decided to re-release the games that would likely sell the best. That's why you hear of all the "blue label" variants for popular games like ALEX KIDD IN MIRACLE WORLD, FANTASY ZONE, DOUBLE DRAGON, etc. All those games have slightly different colors too, and PHANTASY STAR was one of the only games to get the re-release without the label change.
Attached below are the two variants of PHANTASY STAR for reference.