Steps 6-9 in your example aren't correct steps. the Modifier page already tells what channel the Modifer will affect. you don't need to also go to each channel and set things.I just tried it again several times.
1. Select flanger block.
2. Select Channel A
3. Click on the dot on the manual button while holding down the control button on Mac.
4. Click on the source window and then select External 2.
5. Click on the Channel window and select channel A.
So now you have set channel A to have the external 2 pedal control the manual, just for channel A.
6. Select Channel B
7. Click on the dot on the manual button while holding down the control button on Mac.
8. Click on the source window and then select None
9. Click on the Channel window and select channel B.
So now you have set channel B to None, just for channel B.
Save the preset.
Now go back and look at channel A and it will be reset back to All.
Even if you set all 4 channels differently, whatever you set the last one to they will all switch back to either none or All.
I am on Axe XIII firmware 12.
Axe Edit III 1.04.02 RC 1
FC-12 firmware 1.10
I-Mac 10.13.3
Edit: Ok I just went back to Firmware 11.01 and Axe Edit 1.04 and it is doing the exact same thing as I describe above.
This can't be correct behavior. Why even give us the option in the edit modifier of All, Channel A, B, C, or D if no matter what we choose it always reverts back to All for every channel.
if you choose A instead of All, you've already told that modifier to affect A only. it already won't affect B so you don't need to go to B and set None since you've already told that modifier to only affect A.