to "rice" a system you are often changing a lot of "dot files", hidden configuration files on your system which begin with a period in the name. having a bunch of dots (like rice) is descriptive but also can be a reference to a racist term used about tuning asian vehicles.
when linux users use it they're usually just referring to a bunch of altered configuration files which are generally dot files. thus, a rice. but im not sure the term would exist if the racist term hadn't already.