There's no reason to believe the war with the sexes wasn't present. They did still have different technology, though Laplamiz's fleet was under Bodolza, they were still quite seperate from each other, and the Protoculture civil war was still known. Likely the fighting between the males & females was intended as a story element, just never explored due to the constantly shifting episode count & hectic production schedule.
In hindsight we know that the only reason Laplamiz's fleet was a part of Bodolza's was because unification of the two sides during the PC/PD war. Before they they were still seperate militaries.