All of my bettas ( and I have had over 40 in the past few years) have been "rescues" or sympathy ppurchases - whatever you want to call them. I always test the ammonia in their cups and about 90% of the time, the ammonia is at or above a 5.0. A few have been at about an 8 and one guy, his test turned the water bluw which isn't even on the API ammonia chart. Amazingly enough he survived and recovered pretty well (dude in my signature).
Usually the ammonia can be as high as 5-6ppm in those cups.
Or higher. They are pretty hardy but they are not invincible.
Instead of prime, I use Amquel Plus. Every time I use prime I end up with a huge headache.
I'm guessing if you did acclimate very slowly, he may of been very sick but you just couldn;t see it. Maybe an internal infection or just one too many days in poor water.
It always is sad when they finally find a good home, only to be so sick that they die shortly after :(