What’s the calorie need differential between an ectomorph and an endomorph?

None. Somatotypes are a pseudoscience and have been completely debunked.

What role does hormone and thyroid play?

The difference between the “fastest” and “slowest” metabolism in healthy people of the same weight is at most 300kcal per day, which is significant, but couldn’t account for a missing ~3k surplus per day

There are however several conditions which cause the body to simply not to process food (malabsorption is the term to look up), which is what must have been happening to you.

It’s very common for people to misestimate their calories by massive amounts, which is why people are expressing doubts, but what you’re describing is a real thing that happens