At one point I thought it might be possible that they'd have Eclipsa be Toffee's mother (mainly to explain how he knows so much about the wand/spellbook, nothing really indicates that could be possible physically beyond the noticeable size difference between him and Rasticore), but actually thinking about would that would mean I doubt it now.
Mainly for the fact that if the whole monster/Mewman situation obviously parallels real-world issues, you don't want your main villain to appear to be a strong cautionary tale for why you shouldn't let the races mix. We don't know of any other hybrids in the series yet and unless they suddenly introduce more, that kind of thing could create a dumb internet faux-controversy by the tumblr crowd about Star Vs. being racist or something.
Not that it's totally impossible they could do that though; just that there are other ways they could have known each other, if Into the Wand wasn't just indicating their "connection" begins and ends with the Darkest Spell. At the very least if Eclipsa knew Toffee and served some sort of parent/mentor role it doesn't HAVE to literally be "she gave birth to him."
I think there are reasons they wouldn't do it and so I'm not expecting it, but it's still not 100% impossible on the level of "TOFFEE WAS MARCO" bullshit.