So I played around with several iterations of a paper template drawn in Illustrator until I had something reasonably close to what I thought would work: a smallish rack to fit a RotoPax 1 Gal tank, although a lightly larger RotoPax should fit as well with some minor overhang. The design incorporates slots on the perimeter to facilitate attaching bungie cords or straps securely.
Finding the correct location for the mounting bolts was a bit of a challenge. Most designs I saw online used four bolts in a rectangular pattern. These are the obvious (and easiest) mounting points given the subframe design, but I didn't like how close together this put the bolts. I figured it would allow the rack to deflect more than desirable given the subframe is already pretty wiggly. So I opted to mount the bolts on the seat side closer to the sides of the subframe where it would improve stiffness. Unfortunately, the the cross bar in this location isn't flat, which means the bottoms of the mounting standoffs I'd have to make would need to be curved to match the crossbar profile.
Edit (Mar 21, 2017): As I discovered later, the fender itself has the location of four holes used for most aftermarket racks moulded into the plastic on the underside. I used the two locations at the rear, but for the front two I opted to drill a wider stance for the bolts to get more lateral stability. Happy to say that after 5 years of use, this rack has held up extremely well. Plans incorporating a minor mod to widen the side slots are posted in a link in the comments.
A local fabrication shop was able to waterjet cut my Illustrator file for the rack into 6mm T6061 aluminum plate without problem. The resulting part had lots of sharp edges and jaggies to clean up, but I'm not too concerned with appearance at this stage and will likely bead-blast and spray paint the assembly anyway.
Making the standoffs on my lathe was pretty easy. I had some 1" aluminum rod lying around, so I just cleaned it up, bored a centre hole about 8mm dia, and parted them to length. I wasn't sure how high each standoff needed to be. 35mm for the rear and 25mm for the front seemed about right, but this required slightly longer M6 bolts than I could obtain easily and I ended up trimming off about 5mm from the 35mm standoffs. This produced a thick aluminum washer which I ended up using on the front standoffs to obtain a little more clearance. Next time I take the rack apart, I'll measure the final dimensions. It was hard to judge correct spacing with the subframe getting in the way.
Locating the holes in the fender so the standoffs could pass through was straightforward. With the fender mounted, I drilled a small hole from below through one of the forward mounting holes in the subframe. Then I aligned the rack on this point and used its mounting holes to locate drill points on the fender. As long as things were close, I could fine-tune where I needed to centre the standoffs on the fender and trace the larger hole that needed to be cut.
The rear wiring harness interferes with the standoffs and has to be moved. It's pretty tight, so next time I'd probably use 1/2" aluminum rod to give more space for the wiring and to eliminate some of the extra filing I needed to do to each standoff to ensure they sat flat at each mounting point. However, the fender holes are drill now so I'm not going to change this version.
Edit (Mar 21, 2017): I got this powder coated with a hard black polyester that has proven highly durable through 5 years of abuse and with a RotoPax fuel can mounted on top.