Hello Brian Yokum,
Yocto is designed as a tool to build and customize Linux distributions. However, it is not meant for development so bitbake is not looking for changes on the source codes, which may explain why you are seeing your defconfigs reversed to the default values.
The following community document covers how to create an append recipe to change the kernel configuration, so perhaps it may be of help.
https://community.nxp.com/docs/DOC-334088
Regards,