The Hyuman's 'Blessing of the Goddess' helps shape them according to her aesthetic; without it, Hyuman form would end up deviating from her preference. This is why there is still plenty of variance between individual Hyumans, but they all adhere to the same general aesthetic; in manga and especially anime form it's less obvious because everyone just ends up looking even more similar due to artist style, though. This is a standard blessing that all Hyumans get, no matter what. It also helps them process magic through giving prayer to her when casting spells, relieving some of the burden of casting magic from them which in turn makes them more dependent on her; there's also the War Blessing, where any time the forces of Hyumanity fight against any other race, they are blessed by the Goddess with greater military prowess across all catagories; it was a big deal that Makoto wasn't affected when the Goddess Blessing Interference Ring was activated, do remember.
You were close on addressing the older sister being born around when the blessing was fading, but again, it is a blessing that helps adhere to the Goddess' sense of beauty; you can see that Yukiko doesn't deviate much from either parent, but Mari, the younger sister, is fairly different in her facial and body structure, just as Makoto is. In her case, however, she still ended up with good appearance through good genes while Makoto didn't, and those two were born entirely after the blessing had faded. He's not even really a 5 in earth standard terms, more like a 6 or 7 quite frankly, but it's not by conventional beauty standards (eg. he's not tall and thin or has a particularly pretty face, so not 'beautiful' like a kpop star, but rather he's very fit and leanly well-muscled due to his training to near superhuman levels to counteract his naturally weaker Hyuman physiology); it's only in comparison to Hyumans (in text at least) that he comes across as if he's a 2, because it's in line with the Goddess' sense of beauty and he has very little sense of self-worth (which is one of the reasons for his insane magic pool, through the process of zen "killing oneself" he does, which multiplies his existing mana pool; being Hyuman also meant he had a much larger mana pool than any Human).
Hibiki and Tomoki's beauty are why they were stolen (not "stolen", they were just outright stolen), but the Goddess' Blessing was not applied to them. They recieved separate blessings, just like Makoto recieved himself, because that is a requirement baked into the entire premise of taking dimensional travelers; in Tomoki's case, there's the infinite regeneration under the moonlight (likely due to being seen as almost vampiric by the Goddess) as well as the Demonic Eye and the magic capability and capacity of a Summoned Hero, and finally comprehension in Common; in Hibiki's case, as well as comprehension in Common, magic capability, and magic capacity that makes up a basic "summoned hero" package, it was an enhancement to the effect of her natural charisma on a subliminal level similar to Tomoki's Demonic Eye, which ties into the second power she gains, conceptual empowerment; she gets powered up according to people's concept of her, which is why she became stronger and more aligned with Hyumans as she was adjusted to fit the concept they had of her as a hero, on top of her already impressive skills prior to being stolen away by the Goddess. Makoto's blessing was "lesser" than theirs, in that it is a singular facet rather than multiple (including skipping the basic 'Summoned Hero' package), but because of the Goddess' laziness it was actually the strongest, since she didn't discriminate except against the common Hyuman language, granting him a slightly modified Mastery of Words, which is, when complete, entirely a godly-tier power. His elemental affinities and magic casting are entirely his own efforts, as with the rest of his skillset aside from Sekai, which was the power granted to him by Tsukiyomi.
