Question 1 misses the point.

Very rarely does a synonym literally means the same thing.

Your example is a good one... thin and skinny.

The likeness here is only superficial, as in both persons would be on the lower end of weigth for their height.

Skinny does invoke some kind of "unhealthy" in usage:

From, the Oxford dictionary:
adjective

1. (of a person or part of their body) unattractively or unusually thin.

(emphasis mine)

As such, the output is what you would expect if you .. learn about the world, not about transformers.