I'd suggest to leave the Eternabond as it is. I used Eternabond Roof Seal (the vinyl backed tape like yours) over many screw heads on my roof and it sealed everything perfectly. As long as you put a roller on it all will be fine.
FWIW, I also used Eternabond Web Seal (matrix backing) and that tape conforms over any surface irregularity but you have to put a coating on it to make it last.
Both tapes are making a perfect seal and sold me on the use of Eternabond. BTW, if you drive a fastener through the tape, it will encapsulate the fastener as you're driving it. The stuff is beyond great!