- Desperism overwrites the third belief slot rather than being additional or being one of the forced starting beliefs. This means that the first time you Evangelize with an Apostle, nothing will happen. (Second and third attempts to complete your beliefs work as normal.)

Well, that was an unexpected issue. When I tested this mod myself it DID overwrites the third belief, but you can still Evangelize your religion with two Apostles, which add one belief each time. Maybe the newest official update changed something, but I am not sure, and I am afraid that I can't fix this because this part is implemented by Lua Script.


- Not sure if the free city double religious pressure works right. Also, when a free city under Ultimate Despair religion flips, the citizens do exert +20 loyalty but the loyalty is towards the free city, not towards Junko, so they basically become permanently hostile to everything. I'm not sure if this was the intent or not (because it is still thematic) or if it was meant to flip them quickly.

Yes, that was intended. Junko is not an alter Elenor and a ruler, she is a chaos bringer. The double Religious Pressure is working right actually (or maybe it is not working right in your game, I'm not sure), but the effect is not so obvious.
In fact, in the early design, Junko can gain a huge benefit from every freedom cities' believers, such a pity I can't make this happen though.


- You can probably stand to remove the four luxury resources and the project that uses them to generate a Prophet and have a similar thing happen by mimicking Saladin's The Last Prophet ability. It's not too difficult for you to get an early Prophet if you focus on it even without a special project, though (although admittedly Junko will be incredibly dead if you don't found a religion).

That's a historical problem. It all starts with the Desperism trait.
In the very beginning, Desperism was not a belief but a simple trait, which affects the religion you found. But later I found out that this effect is impossible to be implemented. So I moved on to "create a special belief for this specific civilization", and this was not possible too. So I came up with the third solution: Create a belief that anyone can possibly choose in the game, but Junko will be the first one to found a religion, then use Lua Script automatically add this belief to Junko's religion. Because you can't choose the belief that another civilization has already chosen, so this belief will be unique to Junko in every game. Also, if you did manage to create a religion(ex. by cheating) before Junko and choose this belief, you will get all the debuff, as this belief only buff Junko's civilization and debuff every other civilization, no matter who found this religion.