What makes WACUP sound a lot better is the Audio Output plugins and DSP you can use.
Better is always going to be subjective & how everyone reacts to audio & anything else being done to it is going to vary.
My overall stance & which was what winamp generally did is don't mess with the audio unless you have to which minimises the effect that the whole decoding process & whatever may go on once it's been passed onto the audio output can introduce - once the OS gets it then who knows.
Trying to route audio through WACUP can get messy quickly. Sure you can you use linein/virtual audio cables but you're still reliant on what the OS/other programs are doing & if you're using a general audio solution to do things I think it'd then likely end up with even more re-processing being done.
As for youtube specifically, the browser version & what WACUP is able to access & play does vary (with MP3, AAC & Opus all being involved) & along with what video encoding is able to be accessed can also affect what audio stream & it's bitrate is obtained. That might also be what's making things seem different as actually different audio is being obtained along with whatever the browser may then be doing to things as part of it's decoding / playback.
-dro