How about putting the sub on the side right next to the one in the front? If they are identical, the center speaker can straddle over them.
In my opinion, Audyssey would not mess with the minidsp's EQ that much because it would apply the filters as required only. So if the mini has done a good job, Audyssey should in theory, leave things alone, or do very little, and there is nothing that cannot be easily fixed using the App anyway. If Audyssey does mess things up, the REW graphs will show it, you could then either use the App to fix it, or limit the Audyssey EQ range to 20 Hz again. You have the choice and final say based on the results. I don't know why the help video you watched would preclude trying it both ways. I spent many hours playing with using minidsp only, Audyssey only, and both, and I got the best result by using both. However, I found using Audyssey only was good enough for me such that it is not worth having the extra wires laying around, so I stopped using the mini. Now that I can use the App, the results I managed to achieve in a few hours is much better than I thought would be possible. By the way, my room isn't that good at all, you can see it in the graph Audyssey on vs off:
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You are getting good results as it is now but I do think from 100 Hz up there is room for improvements. I just thought you have too much of a drop going from 20 Hz to 240 Hz, a little boost to the mid bass wouldn't be bad.
If nothing else, I think even just lowering the subwoofer levels by 3 dB should help narrow the gap and improve the balance too. That being said, I am just commenting based on the FR graphs. At the end of the day, if you prefer the way your bass response sounds now, then you are good to go.