OK... I think I know exactly what happened now.
in the wiki the instruction is missing an important part and that is to first copy the default savedconfig file and then change it with menuconfig. As the whole reason of using savedconfig flag is only to tweak small number of options (right?) I think it's appropriate to use the current config as the base.
portage system also acted very strange.
first of all I was expecting that when I delete the savedconfig use flag it would replace the savedconfig file for me but it didn't and just left me with a broken config file.
second, I assumed when I rebuild the kernel it should just delete the old modules directory and make a new one but no, it only installed the new modules and didn't delete the old ones. this looks like a bug to me but maybe there is a reason for this behavior? idk...
after deleting the modules directory everything went back to normal. after building gentoo-kernel I get a message telling me that it did in fact use the savedconfig file. before deleting the modules directory it didn't print it.
thank you zen_desu for your help and also for your awesome initrd tool )
I'll mark this as solved now.


