The Visa PLUS logo means that the ATM is connected to Visa's interbank network built specifically for cash withdrawals across banks, i.e. a person using a Fidelity card at a non-Fidelity ATM. It actually isn't the same thing, from a technological standpoint, as a merchant accepting a Visa card when you buy something.
My guess is Fidelity filters all ATM withdrawals in their system by Visa PLUS (or whatever data line comes out from a Visa PLUS ATM transaction) then reimburses those lines. Why Fidelity may not be charging accurately is the transactional data is messy or the filter is too broad, or maybe both. My problem here is that Fidelity is probably trying to fix this issue, whereas Charles Schwab refunds all fees outright (maybe by checking withdrawal amounts outside of normal increments, e.g. $20 or whatever it is).
That'd be my guess.