I've flown Y (and more recently a bit of W) for work for years. It's really no big deal. If you can't sleep, watch the films or listen to an audiobook. If you're cramped, walk around. Usually in Y I doze a bit, I have certainly had as good a sleep in Y as in some premium cabins.

On the other hand, anyone demanding I fly long haul Y is going to pay for a rest day on arrival, and if I fly weekends to get costs down, I'm having them back as days in lieu. There's a quid pro quo here, and the "it doesn't add value for our customers" is the weakest possible argument for building a cost saving mentality within a business. It's treating employees as cost items rather than value adds.

It seems your company has a reasonable policy in allowing self-upgrades, that's more than many have, as the spend is channelled through an OTA via Concur for a kickback, and you're pretty much stuck with that. I would tend not to try to game the system by using high cost flex Y fares as a basis of comparison, just take the best options under the constraints you're under and work from there.

But you took the job, the job is presumably rewarding in other ways. There are certainly employers who will fly you around in J, and it's an open jobs marketplace. So look at why you took the job in the first place, and if the travel policy isn't good enough, vote with your feet.