ConfigMaps offer everything I need for a tool like konfd, and ConfigMaps work with the majority of clusters deployed today. While I could have used a ThirdPartyResource, that would require me to design a custom scheme and write a little more code up front.
Also, there are a few issues [1] with ThirdPartyResource objects including the lack of validation and inconsistencies when interacting with ThirdPartyResource objects through the Kubernetes API [2]. That's not to say ThirdPartyResource's should not be used, but it's not a decision take lightly.
Now, if konfd were to grow or add more features, then I think a ThirdPartyResource would be the way to go -- mainly because ConfigMaps require the use of "reserved" keys and annotations to configure behavior.
[1] https://github.com/kubernetes/kubernetes/issues/22768
[2] https://github.com/kubernetes/kubernetes/issues/29542