Is it odd to hear somebody in a country says to somebody coming back to the country "have a safe trip back home"?
Sounds good to me, but is this a sentence used when you see somebody off?
Odd? No. The only thing I am confused about in your post is that you said "... somebody in a country says to somebody coming back to
the country..." - to which country? Their own or the country they're currently in? It's a little ambiguous.
The person speaking is either speaking to someone who is leaving or speaking to someone who will be arriving soon.
Imagine these two conversations by phone:
Person 1 (in Spain) : I'm going back to Brazil tonight.
Person 2 (in Spain) : Have a safe trip back home. Hopefully we will meet again one day.
(Note, this only works if Person 1's permanent home is Brazil)
Person 1 (in Spain) : I'm coming back to Brazil tonight.
Person 2 (in Brazil) : Have a safe journey [back home]. I'll see you tomorrow!