... This is already moddable, plus, muslims seem to be able to marry nestorians.
Anyone can marry anyone so long as they are a courtier in the court of yourself or someone as the same religion as you - nestorians mainly exist in muslim areas, so this is likely what you are seeing. Its also possible that some religions have specific exceptions, but as far as I know that ability is unused outside of the pagan religion in vanilla.
This actually leads to the odd situation where you never see plausible intereligious marriages like the (historical) ones between Iberian rulers, or the Turks and the Byzantines, or any group of christians and the local pagans, but every now and then you get requests from someone asking you if they can marry some lowborn heathen who somehow ended up in your court.
I would also say that just because something is moddable doesn't mean it isn't an issue. In this case, yes it is moddable, but doing so takes time as its not simply a switch like 'can marry heathens = no' which you change to 'can marry heathens = yes', but rather you have to do so for each individual religion and say which religions they can marry. Secondly it isn't even particularly useful to mod, as doing so leaves you with the problems that were before you couldn't marry heathens, as there is no nuance to the limitation, its either there or it isn't - there may or may not be a general penalty on marrying wrong religions if it is allowed (its been a while, I can't remember) but even if there is, there is no distance limitation so enabling it means its as easy for say the king of scotland to marry the queen of mali as it is for a turkish sultan to marry a byzantine princess. Adding nuance here is impossble because these modifiers are hardcoded; in some cases you have the choice of having them enabled or not, but there is no way to change them or add new ones.
And of course, just because something is moddable doesn't actually say whether it should be changed or not in vanilla. Paradox constantly alters things that are moddable to change the balance of the base game, that something can be changed by a modder isn't inherently an argument that it shouldn't be changed by paradox.