Raymond,
It feels like a rubberized type coating with a slightly rough texture.
But, your statement that when you bought yours (cap and seal together I assume), it came with a cork seal, answers my question.
Because either your seal did not have this coating at all, or it was on the side you could not see and your cork side is exposed.
Therefore, I'm sure it is OK and correct to put the cork side so it is exposed and contacts the filler neck.
Pretty much what I figured, but I love discussing these very small details.
Thank you.