There seems to be a lot of confusion.
Padding is common in nicer backpacks now, but deciding between a courier bags and backpacks on the basis of padding is missing the point.

Are asking about bike specific backpacks, or regular backpacks?

Are we comparing regular messenger bags or high end customs?

I ride a red demartini of unknown age, great.
I used to have a black manhattan portage with grreat sentimental value until is disappeared with about a pint of my blood after an accident.
I also had a timbuk2 (not a fan).
And an orange vinyl chrome kremlin. Too long, wrong dimensions, Roland has the specifics.

I find the backpacks are lousy when empty or leaning over.
The courier bags are lousy when super full or upright.

The backpacks shift around or binds your shoulders and is a loose bag that shifts its load all over the place.

All in all courier bags are best for the kind of riding I do, but not the chrome.
I will either buy a bailey, reload or a local custom.

Try and buy something local, it is very easy to make a demartini style bag and it would be good to support local crafters.