Your logic is broken there somewhere.
In fact he specifically said "I fail to see how this will make the Ubuntu Phone more appealing to the average user." shortly followed by "my point was that this will remain a niche phone."
-Edit to remove somewhat unnecessary snark-
I don't think 'your logic is broken there somewhere' is all that snarky in the grand scheme of things, in fact it's a pretty clear statement of fact. The two things "terminal apps are not appealing to average users" and "this phone will remain niche" are absolutely not logically connected.
Since you can assume that the terminal will be never or very rarely used by average users you can make the advanced functionality available as command line applications and leave the most basic/common options in the GUI.
A naive user is far more likely to check a box and click apply by accident than they are to type "rm -rf /".
A good example is a modern version of Windows, the control panel is full of options,tabs,checkboxes etc that can do weird stuff to your system and consequently make it harder to use because (until recently with powershell) windows has never had a useful commandline.