So I did a bit more experimenting yesterday with placement and I think I've got a solution that works. I also learned a few more things that might be helpful to anyone else trying to mount an Ortlieb QL3.1 bag on a QuickE+ 2019.
For anyone else trying this, the following may be helpful.
1. The Ortlieb bolts have the same thread diameter as the mounting holes for the MIK deck, so you can just screw the mount directly to the MIK deck holes. This may work well for people with smaller feet than me, who don't want to buy the MIK deck.
2. The rails on the MIK deck are smaller than the rails on the factory rack (the 2019 rails seem to be a larger diameter than the 2018 models). You will need to buy the additional clamps from Ortlieb if you want to clamp to the factory rails -
https://www.ortlieb.com/us/e190
3. The angles on the stays for the factory rack , make it very hard to get the QL3.1 to fit if you need to mount the bottom attachment point of the QL3.1 behind the stays, as you most likely will if your foot is larger than say an EU 42.
4. You can't mount the QL3.1 clamps upside down (with the bolt above the rail) as the leverage this creates makes the QL3.1 mount rotate regardless of how tight you torque them (and Ortlieb only spec's 1.5 nm, so you shouldn't really do it up particularly tightly.
5. There is very little space in the middle of the MIK deck to fit any kind of clamp in (including the QL3.1 clamps, however, you can get them in there and once you tighten them, they rotate down into a better position.
6. If you do put the clamps in the middle you need to be careful when tightening them, as the bolt protrudes out of the rear of the clamp and scratches the factory rack (learned that lesson the hard way, but you cannot really see it with the clamp in place).
After a lot of messing around, I realised that the main issue was actually the bottom mounting hardware, which uses bracket to sit behind the rack stays and holds the bottom in place. The problem is that this is really not made for stays as large in diameter as the Giant factory rack, so needs to be offset quite a bit to the rear. It seems to fit okay if you put it in front of the stay, but this won't give your ankle very much space, and you'll probably still get the occasional heel clash.
The end solution was to remove the bracket on the bottom mounting point and substitute it for one of the larger clamps that I had already purchased (but didn't actually need as the top of the QL3.1 was clamped to the MIK deck with it's smaller rails. This actually gives a better mount than the standard QL3.1 and looks much neater as well. I did have to buy a longer bolt for the clamp (40mm to replace the Ortlieb 35mm) so that it was long enough to fit through the QL3.1 hardware as well, but I've got a really nice solution now.
I did try turning the MIK deck around, which gave a bit more support to the top rail of the QL3.1 (and offered more rack in a more usable position rather than squished under the seat), but I ended up turning it back to the recommended position as I'm thinking of getting a MIK bag for the top, so decided to leave it as is.
Thanks again everyone for the good advice, and I hope the above is helpful to anyone else wanting to use a QL3.1 bag. It was a real hassle to make this work, but I love not having the pannier mounts on the back of the bag which makes it much nicer to carry around when it's not on the bike.
