The idea as I understand it is that certain bonuses overwrite each other (indeed in the picked order). Examples already given above.
I'm more in favour of fixing the issue in favour of letting all picked things apply fully- natures, as I see it, are separated for a reason- with all in one pot, I could combine proselytizing, dogmatic and warmongering, which would on the one hand be quite powerful to spread, and on the other hand totally lack flavour (which is currently more defined over the picks in doctrines)-
To stick with the given example combination, it would be powerful at converting vassals and neighbours, but not at all define what to do they are converted after, as it lacks the more detailed aspects of the faith that are currently enforced on any reformed religion.
If it also serves balance reasons I can't really determine, but the current setup does a good job at also ensuring a reforming AI to have some flavour in their religion.