So it was probably a skill/knowledge thing. And that's very common at these smaller stations. IME the station supervisor is generally a more capable and knowledgeable person and can get these things done. So you can ask for them nicely if the check-in agent is unable or unwilling to do some of these complex requests.

Of course, if there is a baggage allowance issue on a separate ticket with a separate airline - nobody will be able to help you at the end of the day.