You explain it in the same paragraph as saying you don't understand it. Harley started in animation, but has been a part of the DCU proper for over ten years - any similarity to the SF trio ends there. Look at her cardback from the DCUC - her first appearance is listed as her first comic appearance, not the B:TAS episode.
As an aside, there's a massive thread at Mattycollector where one of the guys from Critical Mess went over all of the history of the Super Friends/DCU in great detail, including Alex Toth's connections as mako mentioned, and tons of other stuff. Check it out, it's great reading. I personally never understood the connection that some folks still have to the SF cartoon; I watched it for years, but to me all it did was make me more interested in the comics, where these guys had personalities and history. The fact that the trio didn't exist in the comics made them vastly less interesting.
As far as passing on those two figures...easily. Don't care about 'em. The only reason I'd buy either would be if I wanted the C&C piece for a character, but if this lineup is true it saves me that bother (which will be fun after skipping wave 17 in its entirety...makes it easier to save up for the Legion box).
*edit* And let me clarify; if they make you happy, great! But for me, the cartoon doesn't hold nearly the pull, and therefore the characters that exist more or less only in that cartoon don't either.