I'm a bit late here to reply...I'm Charis w/ Sashco. We make Through the Roof! There is still some of the outdated packaging out there, but it is indeed OK to use Through the Roof on rubber roof membranes. Just be aware that, over time, Through the Roof can wrinkled the rubber a bit. It's generally not noticeable, nor does it affect the seal - it will stick stick like nothing else.
Thought you all would want to know. We have updated our packaging to say that it's OK on rubber roof membranes, but it always takes a bit for it to make its way out into the stores.
If you have more questions, feel free to PM me.