I think at this point nobody is at all clear what question there is left outstanding to answer. If your question just boils down to "Did any Motorola-branded PowerPC processors physically come out of a factory owned by Motorola instead of IBM then the answer is probably yes. I only say "probably" because by the mid-90's many traditional silicon design companies were selling off their manufacturing assets to become "fabless" IP-only shops. However, I'm fairly certain Motorola was still in the business of stamping out silicon up until at least some time after the Freescale breakup.
(Conversely, IBM was still big into owning fabs in the 90's and 20-aughts, which is why there are many examples of chips "made" by other companies that came from IBM factories. For instance, most of Cyrix's 90's CPU designs.)