Couples looking like siblings —> honestly that’s more of an artist choice than anything. There are only 4 faiths introduced in the holy sea, so we are to accept similar hair colors and eye colors as traits of a homogeneous area. I personally didn’t notice too much of this in this manhwa specifically, but I do notice it in other series and I feel like it’s just so a family unit (the father, mother, and kid) all look alike to avoid confusion
Marriage across faiths —> the direct line of a faith comprises of siblings and cousins, and they naturally hold important positions, more so than a lower member that is more distantly related. Like in the previous point, this area of the story is contained to only 4 faiths introduced/ families. Thus, someone high ranked in blue would probably marry someone of a similar rank that is NOT their sibling / cousin, meaning marrying someone from a different family / faith. It’s easier to think of the factions as different noble families, while they may be political adversaries, they also maintain marriage ties.
The second son —> The second son of Eshua is Benjamin, the uncle in charge of finances. He cannot assume the family head’s position due to several reasons. First is the position would naturally fall on the direct line of succession, which would have been Isaac’s father. If recognized officially, this would mean Isaac has equal claim to the seat. Next is support, the two factions within Blue is the patriarch’s and Noel’s support from Gold. Benjamin does not have retainers bolstering his position. Third is interest, we don’t see much of Benjamin Eshua wanting to claim the seat. Last and most importantly, the family head Eli is alive, well, super strong, and thriving. He continues to have great power and influence in Blue and with other faiths. Because of his strong position, he can choose who to pass the mantle to, and since he is alive and well, he can choose to skip and entire generation of his children and pass the seat on to his grandchildren since no one expects him to die anytime soon.

Can someone please explain to me the mc's family, im so confused, why do couples look like siblings, and why would the family head have children with someone from the popes family whom they're enemies with