I would like to point out that on D&D Beyond (the official digital toolset for 5e, coded under the guidance of the 5e design team), when you mark that a magic weapon - say a Flame Tongue, for the sake of example - is your pact weapon, you begin adding your proficiency bonus to your attack rolls, regardless of which patron you have and whether or not you're proficient with the weapon outside it being your pact weapon.