Noticed you never did get an answer, and I am busy scouring trying to find where I found this mentioned. Pretty sure it was in a live Q&A so it makes it slightly harder to ctrl+f.

The system does not push you to cooperate, it pushes you to meet. To be unable to ignore the other.

Soul mates are mentioned here Design Journal 2 Soul Selection Destiny Achievements and Soul Mates

Most importantly, soul mates whose affinity go in opposite direction become diametrically opposed to one another. To that end, there is only one way to get past such an antagonist – separate their soul from their body and send them back to the Akashic Records.

The tidbit I could not find again was the fact that they intended this to create story. To create a dynamic world where anything could happen. If you and your soulmate meet and you are both gladiators that go from tournament to tournament and fight for the crowds. Now you have a synergistic bond with someone of the same intent and your shows in the arena are even more grand. However if you and your other half are on opposing front lines in a war, now you feel a pull towards the enemies side. You don't want to slay your fated brother/lover/rival over some petty border war. I am rambling now forgive me, but here is the points; It is to make the world interesting! If soul mates were always beneficial then you almost Have to go find yours to have a competitive edge. The ability to know your two souls are inextricably linked despite yourself or even in favor of yourself is dramatic, its flavorful, it is engaging.

They spoke about this during the QA from 2-3 months ago. Basically a religion could tell you to murder/sacrifice someone. The act of killing is a dark alignment action but upholding your religion is a light alignment so your actual shift would be the net.

Now that said from how it was mentioned it made it seem like some religions may be geared toward the dark side while others toward the light. If your soulmate follows a religion that demands otherwise “dark” actions I would assume they would end up on the darker side of the spectrum marking you enemies, even though you both do as your religion dictates.

As was said above how you actually react is up to the two of you however the engin will likely pit you against each other in random scenarios it generates. Using you as the opposing trigger and vice versa. But via the soul engine you would likely be forced into confrontation from time to time if you choose to follow your destiny.

Malais nailed it. The developers discussed this in the Player Destiny System Q&A. Your chosen religion and some other factors will effect your affinity, and generally speaking progressing the story opportunities will help your affinity gains.