As there is no way you can have an audit trail for manual flying during line flying then it opens the way for wide spread cheating. That is a common thing in fake logging of instrument flight time on line - no audit trail. As far as simulator logging of hand flying is concerned that means the sim instructor must keep the log which gets messy. And don't forget it is a good bet that many sim instructors are themselves addicted to automation.
CentR Us
You can audit this if you are prepared to use the data available properly, or add cockpit cams. The data on any aircraft designed in the last 40 years will identify if the AP is connected.
IMC vs VMC, cam is the only solution, which would also lift the value of the stabilised approach data when the program has implemented different IMC to VMC criteria.
The addiction to automation is a result of the direction that the manufacturer, regulator, human factors and compliance programs have pushed the operation. It is true that deviations from the automation are much easier for the instructor to identify, or anomalous use of automation modes, but the industry was pushing towards "the promised land" of reduced human error through automation without heeding the warning on the packet (under MSG %...) that distancing the human from the control process loop increases the likelihood of SA failure as we have seen on repetitive occasions over the last 20 years. The loss of basic flying skills, having pilots in a RPT aircraft that would be lost in a C150 let alone a Pitts S1 is so depressing I think I will go and have a quiet sob in the corner over the demise of professionalism in this industry, the final insult of the bean counters, bureaucrats and the shortsighted.
The history of IFLOC in the last 20 years has been an abject disgrace. We originally fell to earth as aircraft filed through inadequate materials and knowledge, then we ploughed fields on the sides of mountains or short of runways, and now we float down vertically in stalls such as AF447/TK1351 to arrive inelegantly in the bottom of a splash or a shallow grave, or more akin to a lawn dart (splashdown) such as Silkair, Flash or Adam air. The disneyland rides given are an embarrassment to the industry, and a direct result of the same industry's direction.