Paying for fees in zkSync Legacy/Lite can be done with STORJ, yes.
zkSync Era uses a new concept called paymasters, which incidentally also could work for layer 1. We are still working on finding a provider to enable a STORJ paymaster, so zkSync Era does not yet support paying fees in STORJ.
zkSync Era is still valuable given the vastly lower overall fees. On the one hand, zkSync Era no longer has the registration fee that zkSync Legacy/Lite had, but zkSync Era currently does not support paying fees in STORJ until a STORJ paymaster exists.