@Celestial-B Of course! I'll start with Harmony:
What's neat about doing characters for webcomics is that, physically, they're already down pat, so she looks really neat! There's not too much happening in the design and it lines up with her personality. Her motivations are good, but everything written after "Trying to find out why some Crystalites's gemstones are becoming corrupt" can be left for a different page about the Crystalites, because it kind of detracts from the central topic of this tab (i.e. Harmony). Her impulsivity is rather interesting. She doesn't get mad at others, but if her impulsive actions are stopped/challenged, does that upset her? Does she concede when her obliviousness is scolded/called out? These are good flaws, but how much of her flaws disappear as she matures in this tale? And, in turn, what new flaws pop up? I love me a good coming of age story, but going from child to perfect adult can be worrisome, so make sure you have some backup flaws. There are bad things about maturing, too.
About her prejudices, would it be possible for her to be prejudice against humans? I know she is one, but she's raised entirely in a system that doesn't favor humans, so would that rub off on her? Give her some doubt, some guilt, some self-hatred?
Now, she rarely gets sad or angry, unless it's for a 'good reason'. Is this good reason what lines up with her morals, or the morals of the readers? There should be times when she's sad or mad because of her morals, but not necessarily in ways the reader can understand. It sounds weird, but that builds sympathy because people can sometimes just break. On that note, I'm not too sure about her. She feels thought out, but a little too perfect, a little too done before. She fills the role of protagonist to a T, but comes a little empty in some spots. I think instead of "she's rarely mad or angry" she should be the person who is really good at pushing those emotions down. If she was constantly battling with these negative emotions and to be happy all the time, you would have a nice internal conflict on top of external. That, or maybe guilt over things she can't control.
Furthermore, the system does affect her personality, in one way or another. Or at least, it should. If she holds it in contempt and resentment, then it is affecting how she holds grudges, though you mentioned she rarely does.
Overall, I do really like her, but I think she needs a little more to shine (gem pun intended). You have a really unique situation happening, and you should use her to take advantage of every part of it. If she becomes a rug and lets people step over her, it's hard to build sympathy. And if she's a hardass, it's still hard to build sympathy. I don't think you're risking the latter, but you are risking the former, even though she is a lovely character.
Now, to Keon! (I'm loving these names, they're so cute and simple)
I like his clean-cut motivation of helping himself, I can see that getting him into all sorts of situations. I love me some angsty boys, but it feels like he has all of the internal conflicts. I can see how he would bounce off of Harmony, however. He could die at any moment, and if she dies that's potentially the end to humans. They're both on this precarious edge and I love it. He feels very desperate compared to her too, where her motivations could be taken at a slower pace. Overall, he's got more happening than Harmony does, which can take away her spotlight. I think he's still missing something, and both characters need hobbies that aren't plot relevant. It helps flesh them out more. Perhaps he needs a spark of something else? I have a lot less to say about him, however, and I think he's well done.
I'd love to see how these characters work together! But I would avoid having too childish of a main character. There are some dark, dark themes floating in this work that could have great commentary on innocence/hardship/coming of age, or the characters could come off as gimmicky and singular in traits, so be careful. Don't be afraid to have your characters do a 180! You don't have to take any of this advice of course, and I wish you the best of luck!