Well in 1989, what else would they have based comics off of? Alien3 wasn't out yet, and Alien on its own doesn't really lend itself to many spin-off comics that couldn't be similarly covered by an Aliens license.
Besides, why wouldn't they have the license for the first film, anyway? It's all owned by FOX in its entirety, it's not like the Terminator franchise where "Terminator" and "T2" are literally owned by different people. It'd kinda be like saying "Dark Horse could make comics based on 'Empire Strikes Back' but not 'Return of the Jedi'." It doesn't make much sense.