Yup, it affects all teams the same. The fact is that the part of merchandise that was taking league, country and world rankings into account was broken, but now it's fixed. I think it was broken since season 11. Also, from now on, it should work properly so everyone should have higher merchandise.
As for OE tax, I'm afraid it is what it is. The numbers for past economy updates are lost so I cannot recalculate. I guess you'll just have to be satisfied with the cash influx as it is.