My self leveling was so thick and strong that I couldn't hardly dent it with the plastic tools I used for safety (so as to not gouge the roofing material). So...I shrugged and put the tape right over it, making sure I had some roofing the tape could stick to.
And 12 years later, 90% of the Ebond tape was still stuck down over the self leveling stuff. I did have a couple edges here and there lift so you do need to climb up there and check every year. And then put more tape over the part that's lifting.
Remember, you can't see the top of the roof so no big deal. But I always tried to make it look good for a future buyer. As it turned out, he thought it looked fine.