Autopilot or not, if you're in cloud or severely reduced vis, the management of the flight takes on a whole new aspect compared to VFR, ie. LSALTS, how to get down at the other end, diversions, and so on.
Logging IFR when you can see as well as if it was a beaut VFR day isn't kosher, in my view, because all those considerations become insignificant. However, once you're in the gloop, the careful planning and good situational awareness are paramount, and the autopilot is neither here nor there - consider an aircraft with a copilot hand flying in cloud; should the captain still log instrument time? Ken oath!