You're looking at the show's breathing room. These aren't bonus episodes bolted on for collectors; they're the cast when the apocalypse isn't actively ending, when Momiji can just be awkward around Daichi without a Natsume trying to kill everyone. The comedy hits because it trusts you've already bought into these people, so it can just watch them exist.

Blue Seed Omake gathers fourteen short comedy extras that supplement the Blue Seed story. The first thirteen appeared on the Japanese video releases of the series, and each one is placed after a pair of main episodes, so the first omake comes after episode 2. The fourteenth was included alongside the Blue Seed 1.5 OVA. These are bonus pieces for viewers who already know the main show.