In PHB, it specifies that if you gain the same proficiency from two different sources, you may choose a different prof of the same type (skill or tool) instead.

Does the survivalist rule for the Scout Rogue in XGE contradict this by stating"-if you don't already have it"? pic.twitter.com/jF1kzoCOyc

— Big Red (@ThisTinSoldier) May 30, 2018

The proficiency rule for backgrounds applies when you gain your background at 1st level. It has no relevance outside that context.

— Jeremy Crawford (@JeremyECrawford) May 30, 2018