That preference option doesn't relate to the playlist editor window & I will probably remove it at some point since it was mostly for testing early on. It just relates to the non-native skinned window frames but as the majority of such windows under WACUP now support it, it's only really 3rd party plug-in windows that aren't able to follow it & just act like they're 1x sized.
Double-size support under WACUP is meant to be enabled consistently for the native windows (main, eq, playlist, video) unlike Winamp which only did it on the main & eq windows (I always hated that inconsistency) so toggling the main double-size option is the way to enable/disable things but it's not possible to do it on a per-window mode (at least not for the time being in a manner comparable to what can be done with modern skins).
The difference in behaviour vs Winamp is to make for a better double-size experience for the majority who want / need things to be consistent.
-dro