I may be too late to help the OP with their decision making process, but I feel compelled to tell my story:
I used to work for a company that allowed us to book economy for short haul and business for long haul. Then I changed jobs and my current employer allows Y only, for any and all flights, regardless of distance or duration. I did not think it would be a big deal; I figured I'd use my status to achieve upgrades for the long hauls.
I figured wrong.
Having done about a dozen long haul fights in Y since joining my new employer, it is absolutely killing me. And yes, to be fair there was a bit of "Flowers for Algernon" at first, but now it's become a bonafide health issue.
So, if I were in a situation wherein a new job opportunity was in front of me and I knew it would require a lot of long haul travel in Y, I would definitely negotiate some kind of exception or allowance, and if I was not successful I might have turn it down.