While it is conventional for the directory structure to match the package structure, and certain problems arise if they don't match, it is in fact not a requirement that they match. This is also true of Java (though a lot of folks don't realize that).
Below is an example which demonstrates this.
groovydemo $ mkdir classes
groovydemo $
groovydemo $ cat src/groovy/com/demo/SomeClass.groovy
package com.somethingotherthandemo
class SomeClass {}
groovydemo $
groovydemo $ groovyc -d classes/ src/groovy/com/demo/SomeClass.groovy
groovydemo $ find classes -type f
classes/com/somethingotherthandemo/SomeClass.class