We investigate by means of direct numerical simulation how large-scale circulations produce deviations from Monin-Obukhov similarity theory (MOST) in the limit of free convection, disentangling the role of large-scale downdrafts from updrafts using conditional analysis. We compare the convective boundary layer to two other free-convective flows: Rayleigh-Benard convection with an adiabatic top lid and classical Rayleigh-Benard convection. This serves a dual purpose: firstly, to ascertain how changes in the upper boundary conditions and thereby in the large-scale circulations modify the near-surface behaviour and secondly, to assess to what extent we can extrapolate results from idealized systems to the unstable atmospheric surface layer. Using a low-pass filter to define the large scales we find that, whilst deviations from MOST occur within large-scale downdraft regions, strong deviations also occur within large-scale updraft regions. The deviations within updrafts are independent of the filter length scale used to define the large-scale circulations, independent of whether updrafts are defined as ascending air, or as air that is both ascending and positively buoyant, and are not due to changes with height of the updraft area fraction. This suggests that even updraft properties are not just determined locally, but also by outer scales. Cold, strong downdrafts in classical Rayleigh-Benard convection notably modify the near-surface behaviour compared to the other two systems. For the moderate Reynolds numbers considered, Rayleigh-Benard convection with an adiabatic top lid thus seems more appropriate than classical Rayleigh-Benard convection for studying the unstable atmospheric surface layer in the limit of free convection.