While you really shouldn't try to understand the OnePass Program without a law degree (and even then, it still might be challenging), you are correct.

In the EWR-SFO market, $278 + tax is the lowest fare, which is I class.

For full EQM, there's a $318 + tax U fare, a difference of $40.

So, I'm guessing that your trip is pricing I one way, and U another (because of availability), which would give you 50% EQM one way, 100% the other. If you want 100% both ways, you'd have to pay the extra $20 or book online.