Which option was chosen for the Linux kernel?
These days there is a package that builds the kernel for you, but it relies on the "savedconfig" system to just save/load the entire kernel config file instead of using USE flags. So you still have to root around in the config menu yourself to change things.
In my experience Linux is very good at correctly declaring dependencies between options, and still working with options disabled, so this isn't as much of a problem as it seems to be for Chromium.