I fail to see how that can occur. The fuel pump is operated via a relay which effectively isolates the PCM from the pump power circuit.
I would have suspicions about their analysis until they could demonstrate, graphically on factory diagrams, how that could occur. I could believe a different explanation, but apparently that's not what you were given.
It sounds as if their part-changing prowess may exceed their diagnostic ability, or at least their effectiveness in explaining the problems.