Although this may be better answered by looking into ancient ship building methods, we can also attempt to answer this from chazzal.
See Bava Metzia 40a
באתריה דמר חפו בקירא ולא מייץ טפי באתריה דמר חפו בכופרא ומייץ טפי
חפו בקירא. טחו החביות מבפנים בשעוה כדרך שעושין אנו בזפת: כופרא. זפת:
So we see that zefes does not completely prevent absorption and can actually be penetrated. In contrast to wax which prevents the absorption.
Therefore a second insulating layer was added on the inside to help keep out whatever water made it through into the wooden hull.
Another possibly relevant source about Zephes: In Maseches Keilim chapter 3 mishna 7 we find that Zephes can not be trusted to maintain it's structural integrity in boiling water and can melt. See Bartenura here:
שהזפת ניתך ונמס במים חמין.
So according to the opinion on Sanhedrin 108b that the waters were actually boiling we can suggest why a regular coating of Zephes wouldn't be trusted. Of course we would have to assume the second layer would help.
That's why I only say this is possibly relevant.