I started with an existing .config that came with the kernel sources or the distro. It clearly is not practical to evaluate each option as there are thousands of options and not all combinations work together.
The issue for an interactive software tool is that the kernel options keep changing every 2 months as new kernel series are released. It would be labor intensive to keep such a tool current.
As for extraneous warnings, Linux is a bit zealous about logging information. It is more likely that “tweaking” the kernel .config will break unexpected things before the offending warning is silenced! Try setting loglevel=2 in your kernel arguments to silence some of those (boot) warnings.