Bump. Come on folks, someone has to know how to do this.
I have no idea myself but I'm guessing it involves either a triple wall pipe with the dirt touching it or flashing to keep the dirt and EPDM just barely away from the pipe. Just above the dirt I think you'd put what's called a storm collar which hugs the pipe and guides rain out away from the pipe and onto the roof. Here's a view of a "normal" roof to see how the flashing connects to the roof and the storm collar sits just above it to protect it from having rain run down between the flashing and the pipe. pinterest
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Triple wall pipe passing through a EPDM roof pipe boot then glued your EPDM roof membrane would be fine.
And then you can put dirt on top of the EPDM. Now, you might also consider putting another flashing on top of the soil if you're worried about washing out but I don't think it would concern me. Depends on the roof slope.
10 Podcast Review of the book Just Enough by Azby Brown