I'll say this one more time. Comfort is a function of fit.
It's going to be different from person to person and sneaker to sneaker.
My most comfortable footwear are my semi bespoke shoes, because, surprise surprise, they fit in all the right areas.
I like these though.
There's truth in this but cushioning plays a role - makes your feet / legs less tired at the end of the day because the impact is better absorbed and distributed. That's why people don't run in bespoke leather soled shoes.
Also some shoes just have more democratic shape / lasting. This is true of RTW dress shoes and sneakers.