If you tape your panels to a rubber roof, it will only be as secure as the glue that holds the rubber roof to the sheathing. I would not trust it. I've seen too many posts from folks dealing with ballooning roof membranes.
I used the Renogy mounting brackets. They are sheet aluminum formed into a Zee shape. 4 brackets per panel. I layed down a generous amount of dicor, placed the Zee foot on the Dicor, screwed them down making sure at least 1 screw per bracket hit a rafter. Then covered the screw heads with more Dicor.
The only problem I have with the Zee brackets is that you cannot get the panels lifted up without pulling them up off the roof. And they are glued down hard, and I would probably damage the rubber roof trying to get them loose. If I ever have to do this, I will simply cut the vertical leg leaving most of it standing up from the roof. Now it is an L bracket, still screwed and glued. Then I would make some more L brackets to attached between the standing leg and the panel. Which is what I would do from the getgo if I was doing this again. I may never have to lift a panel anyway, so may not ever be any issue. I am confident that the brackets will outlast the roof membrane and never leak.
For the cable I simply drilled a hole through the roof down into an interior wall. Fed my cable through and then sealed the hole with Dicor, building it up as a flashing. I did not see any need for any J-box or actual flashing. It's only about a 5/8" diameter hole and is easily sealed with the caulk. I used the type of cable that is a red and black conductor in an outer UV rated sheath. Not individual conductors. I left about 3' of the cable above the roof line, formed it into a drip loop just above the Dicor pyramid, and then assembled my MC connector. From there it is extension cables that I made up in whatever lengths needed to go between panels. Extensions cables are extremely easy to just make up whatever you need.
All the cable inside is within walls. Pretty easy to fish it down to the basement, which is where the controller lives.
Like others, I used some Eternabond tape and some Dicor blobs to secure the cables to the roof, just enough to keep them from flopping around and grinding away at the rubber roof.
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