Like what Panon said. Remember that the gunpod cannot be reloaded in the field. Roy probably used up his last one with his battle with Ivanov, so they were carrying another one for him to take after he was done refuelling. Convienient I'd think. Refuel and reload.
And about science vs magic.....urmmm....since when did Macross ever wanted to be "hard" SF? Others already mentioned the fantasticalities of Macross so I won't go there. Enjoy the show.
PS: On unrelated note, I like the Japanese engrish term, ESPers, which is basically psychic people, who can use ESP. But technically, ESPERS would just have ...well..ESP, and not necessarily telepathy, nor telekinesis or empathy.