The issue appears in both genkernel and genkernel-next. When used without arguments or configuration change (genkernel.conf) the genkernel runs with --mrproper option (defined in genkernel.conf) as a result if a user wants to run genkernel with --menuconfug the kernel config file ".config" wont change. Make mproper deletes the configuration changes and the already compiled objects. it's similar to make clean but it also deletes the changes to the config. It is very unpleasant to see this enabled by default. In many cases it leads to greet frustration on the user side. This option should be disabled as soon as possible.
please open one ticket per package, because it has different maintainers.
change genkernel to (only) genkernel-next the exact configuration: # Run 'make mrproper' before configuration/compilation? MRPROPER="yes" file: /etc/genkernel.conf installed by: sys-kernel/genkernel-next
Package removed.