It's still a personal choice. You can remain within company policy but choose to upgrade (miles, cash, whatever), or if you can't afford that, find a job that suits your needs.

I wouldn't take a job involving frequent travel if it meant I was going to be sitting on a plane miserable for hours at a time (and at 6'3 that's anything over a couple hours these days with seats being as tight as they are).

Travelling with work colleagues (and I include bosses in that) you can easily explain your upgrade if asked. It becomes a little more difficult if you are travelling with clients... who may be paying your fare. That may trigger some questions (via your boss or contract manager) that can't be explained at the time (a client isn't going to ask you on the spot why you are flying business if their contract with your company only allows for economy).