No, Amazon segregates its own inventory from FBA inventory for items where Amazon.com is the seller. FBA inventory only gets commingled with other FBA inventory.
Supposedly Amazon now maintains separate inventories for each FBA vendor at some but not all of their distribution warehouses (like their San Bernardino facility).
Amazon used to be a client and I've personally visited their San Bernardino facility and seen firsthand how FBA inventory is segregated from Amazon.com inventory.
Note that the WSJ article is from 2014--several years before my visit. I can't speak to what Amazon was doing with inventory in 2014, but it sure isn't what they were doing in 2017 at their SoCal distribution facilities.
Supposedly Amazon now maintains separate inventories for each FBA vendor at some but not all of their distribution warehouses (like their San Bernardino facility).