Is it true that one can say Afiyet olsun even to someone who has already finished eating? I think I have heard this a few times (even in a restaurant when the customer is leaving) and dropped my ears because it sounds funny.

Yes, That phrase can be said before, during and even after the meal. Flexible phrase. Yes, when the customer is leaving a restaurant you can hear the restaurant workers may say Afiyet olsun to people,  along with  saying goodbye.

-İyi günler. Afiyet olsun. Yine bekleriz..etc..

[Have a good day , bon appetite..please come again..]