You are right - the ONE & ONLY place, where LCY code -in your case EUR- can be entered, is GL Setup.
LCY must NOT be added to Currencies table for whatever reason, that will cause unpredictable system behavior. Nonblank Currency field all over the NAV system is widely used to trigger the workflow logic.
The same refers to another place, Countries table, and especially with the EUR currency - users are willing to indicate EUR there for Eurozone countries, despite they themselves belong to Eurozone or for some other reason they have LCY=EUR. However, if EUR is not added to Currencies, it is impossible by design.
Which AddOn requires LCY to be present in Currency table? HOW then the developer of that AddOn got it registered?