Yeah I guess in order to make this into a simulation, one would effectively add all the exponential time back, since it requires all that to "run" an amoeba on a classical computer. In that article they mention the organism communicating across its body, i.e. reacting to stimuli in all parts in a correlated fashion, that is the bit referring to a quantum system. Of course all physical systems are quantum systems (if I actually had a phone that one too yes, although the operating system does not make use of its nature). So there is no question whether we can simulate that algorithm, it cannot be possible without calculating all the parts, and that is no longer linear time.