Again, I don't think I'd classify having only two women at the same time as a "harem", but I won't try to split hairs here. I will say that just because you can get scenes with two different LIs at the same time doesn't really mean they're OK with it. You're not really on the "Vanessa route" if you're also pursuing Ellie. You're on a multi-girl route, one that may or may not be possible.
I could be wrong, and you might be able to be with both Vanessa and Ellie; but you just as likely could destroy both relationships and end up with nothing. I'm not telling you how to play, ofc. I'm just stating that I don't see how Vanessa would be fine with Ellie being the MC's lover in addition to her, and I'd expect her to be pissed when she finds out and probably dump the MC. But maybe she'll surprise me.