Odds are, and this is just speculation... but your only advantage to already having your Zeta done is that you will be able to use your Zeta as a base for the new relic, instead of need a crafted base for the new relic. If you don't have a Zeta (or potentially just a relic at any stage) then you'll need a new crafted base weapon or something for the new Weapon Quest Line. Again just speculation.