Nice Grump, here is another idea, I secured my panels down with Well Nuts, they are 3/16 x whatever your roof thickness is. You drill the 3/8" hole after marking the spot, and put the well nut in and when you add the bolt it compresses the insde flexable rubber against the inside of the roof material making a fantastic seal. But I didn't stop there I put roof repair tape down first just under each foot to give it better support on the top surface, incase the bracket wanted to cut my TPO, I have the extra thickness. After attaching all this I added the sealer to all as you can see in the picture. As far as going through the roof, see the area between the two vents, that is a 4 inch vertal wall which makes up one side of the bathroom. I went that route through the roof then through the floor and to the controller. I got a 90 degree plate for the turn down which is made just for this. I'll include a picture when I'm home as I could not find that one right now.
The second picture shows where I went through the roof, sorry it's not exactly a great picture, perhaps I can get a better one. But it gives you the idea. Maybe you have a similliar layout where you can also investigate for a turn down.