A repair shop will recommend taking the complete rubber roof off and replace the sheet of damaged wood, then replace the epdm at the tune of 4K to 6k. They wont warranty a patch, or wont consider it. Your insurance adjuster will most likely come to you and write it up the same without you having to take it anywhere. I've known 3 other friends who had similar incidents and the insurance wrote them a check for the complete replacement with no questions asked. One of my friends got 8K and kept the money then did a patch repair as what your thinking of doing and used the remainder for his personal use.
As far as the question of repairing in the manner you stated, I'm sure that would work as well as any other patch method you choose. Eternabond is very good stuff.