Lossless codecs are lossless all the way, not only when you decode them back to wav. If they were, who would and why use them? You have .rar that is better for these purposes
The cause of difference in sound when playing flac/ape/wv compared to wav is the plug-in.
FLAC doesn't have CBR, but VBR instead, why? Because some (more intence?) parts of the track are coded (archived) with the bigger amount of data, some parts (like silence?) don't need that much data. That is done to save space, time, resaurces.
I'm not sure, but I think when you play FLAC, your player decodes next 10seconds of the track to wav or something like that.