it is safe to assume that when you are hungry again, you would eat the second one. It is a BOGO offer, not a buy one get another item of your choice offer. The "value", or cost, which you are assuming, is pretty much not an issue.

I would never dream of asking an establishment to substitute for the second item of a BOGO. However, if I did, and they said no, I would count it as an odd request and move on. They had an offer you couldn't or wouldn't take advantage of. That is on you, not them.

Your assessment that the substitution is "reasonable" sounds as though you are taking on the responsibility of the manager. However, you were on the front side of the counter, not behind it.