I could be wrong on the critera, but it seems that if you have a modified config.txt and/or cmdline.txt and you then perform a kernel update that switches branches (ex. rc to mainline), the files are replaced with the default version. Other kernel updates leave the existing files untouched.
Is this intentional? I would much prefer a .pacnew, than to change the files. I test kernels often and sometimes forget to replace the files before rebooting. The default files are not always usable, ex. nfsroot, usb quirks, or expect to have an overlayfs in place. But worse, is a successful boot and not realizing you are running on the incorrect configuration.
Edit: The update does notify of the file change, so it is my fault for not resolving the issue. I would just rather not have an issue to resolve.