If the OVMs work as they are expected, you can do the refilling at the machine itself at the subway station and not have to worry about if online refills take or not.
I think that the ability to refill at 7-11 stores, Walgreens, Duane Reade and other merchants will remain in place. The only issue there is that many of the store personnel don't know or have trouble doing the refill at the register.
My own intention is to continue to use my reduced fare MetroCard for as long as I can (before the expiration date on the back) before switching over to a reduced fare OMNY card. While I would register the card , I would do the refilling at the OVM .