Hi Jim,
We have TPO on our roof, too. When I started researching the installation and sealing of the roof when I was going to install our solar panels, I found out there are two (and possibly more) types of TPO out there.
One has a fleece backed surface to it. The other appears similar on both sides of the membrane. We have the former on ours and when applying a sealant (Dicor or other brand) to it, you need to apply a special primer to the surface just before applying the sealant. Dicor makes it, called Ultra Sealant Primer. Then you can apply any self leveling sealant to the primer.
If you have the TPO membrane that does not have the fleece backing then they recommend using the Ultra primer and their a special sealant called, Ultra Sealant.
I believe this procedure and the products has to do with the expansion/contraction/shrinking with age of the dis-similar materials. But, I was never able to verify this for sure.
Now as far as using Eterna-Bond on it, I don't know if it is recommended to apply the primer first as well, but according to their website, it has built-in primer and all that is needed is a clean surface.
Which method you need to use depends on the size of the hole. If its narrower, you could use self-leveling sealant. If its bigger, use Eterna-Bond.
Good Luck,
Tom