If I'm understanding this correctly - and the Mechanics team can correct me if they like, this is how it works.
Everyone starts with one traditional element. You can then spend 1 pp to unlock another element and 1xE + 2xD specialized jutsu for that element. OR you can spend 1 pp to unlock TWO elements and acquire 1xE + 1xD jutsu for each. This element may be a 'new' element [requires that you already have two elements], or just another traditional element.
The traditional elements listed under the Jutsu Creation rules have specific specialties that cannot be changed. Unlocking Yin or Yang jutsu for your character allows you to adjust those specialties how you wish - representing that Yin and Yang function differently for everyone. Unlocking a brand new element also allows you to adjust those specialties how you wish.
In the above example, with the Jikodo: the Jikodo is paying 1 pp to unlock two elements [Sand, and either Earth OR Wind, one of which is covered by the initial element you start with] as well as 1xE and 1xD techniques for both Sand AND whatever element they unlock.
In the case of the Anju [Gift of the Hermit Group], the Anju is paying 1 pp to unlock ONE element [which they can apply a specialty to, because Yin and Yang do not have listed specialties - in this instance, they are choosing Damage and DR Ignore], as well as 1xE and 2xD techniques for that element.
The additional upgrades allow you to make more custom techniques for that element.
I BELIEVE that the custom techniques you make do not need to be paid for in RP Tokens - but I could be wrong. They still need to be learned, like other techniques.