I read the the complex endorsement involves being instructed in
retractable gear, flaps and constant speed prop. I'm learning to fly
in a C172, which has flaps, so it seems unusual to me that flaps are
specified in the complex rating given that I have been using them
since day one.

The only reasons I can guess that this is pointed out are that A:
people learn to fly in planes without flaps or B: flaps are "one more
thing to worry about" and so the definition includes all three to make
sure the pilot can handle multiple things to worry about in the small
amount of time one has to land a plane. I'm leaning toward B but
thought I'd ask here.