For the actual travel, you'll get the same service. However, a few differences in the fares would be:
-Fare options (maybe refundable, or the fees are different to make changes)
-Different cost to upgrade using copay/miles (as you noted)
-You'll get 150% of the mileage toward elite status for Y/B fares and get 2 elite points. With other non-BusinessFirst fare classes, you'll get a maximum of 100% elite mileage and 1 elite point (to count toward your elite status)