I ran into the same issue with my metal barn roof where the service entrance mast head was leaking water as the former owner had jerry-rigged it with tar that had cracked over time. The mast head exited right next to one of the metal roof seam overlaps. I found a mast head roof penetration kit that was designed to solve that problem. It used a very flexible aluminum surround bezel about 3/4" wide at the edge of the rubber boot that you can easily bend and form to follow the contours of the metal roofing seam. It came with self tapping screws & washers that you were to then use to screw through the aluminum bezel from the top into metal roof and seal with silicone sealant under the flange area to make it 100% water tight. Since I replaced it, never has leaked a drop with rain, snow or ice. The only catch is you would need to find one in that style with the fire/heat retardant rubber boot. You might be able to devise one using a tent stove jack & using thin strap-like material in aluminum, brass or copper to conform the edges of the boot to follow the roof contour if its not too radical a contour and then screw & seal it in place.
Edit:
This is what I used on my roof electrical service entrance mast head penetration. Its rated for 212F continuous/ 275 intermittent. Not sure what your exhaust pipe temp would be at that distance. After I installed it, I painted it to match roof and for added UV resistance for the rubber boot and it turned out quite nice. In the beginning I wasn't too sure about it as it seemed a bit flimsy with the cut-to-fit circles for various diameter pipe and with the seam that clips it together, however after it was all screwed down, sealed and buttoned up it seemed quite stable and tight.
