I thought I saw something that covered this but can't find it.
What happens when you're given the same proficiency from multiple sources, such as the Healer origin and the Medic class.
In base5e they allow you to pick another tool proficiency when given 2 identical tool options but say nothing about any other type, and the only other thing that sort of mentions this is the usual "only 1 source of 'vantage counts" when subject to multiple instances of the same type.
Given every class in this game has at least 1 ideal background origin, it's seems counter-intuitive that you would punish people for going the iconic option by forcing them to lose a proficiency.
Now maybe if you don't want to provide an unrestricted choice in this instance the option would be to go back to base5e and give the SG classes a choice of 5 or 6 class skills of which they get to choose 3 to be proficient, which would remove 99.99% of all problems and give folks a greater ability to customise the feel of their characters.