For a series with such a romcom-esque premise, I was expecting something silly and over-the-top. And, to some extent, it is over-the-top, but it's also surprisingly earnest in its delivery.
Notably, rather than a story about a girl trying to hide her true self, it's more a story about youth and balancing how to be both true to yourself as well as kind to others. It's also a story that's unfailingly kind to its flawed characters, even the antagonistic ones.
Hoshino, the main heroine, isn't actually ashamed of how she normally looks--and neither is she putting on airs in her school life. More than anything, her makeup is the armor that gives her confidence in her relationships. Kobayakawa actually learns to be a better person from her, rather than the other way around (which seems to be the usual tract these stories take).
The story also tries to deal with bullying in a meaningful (albeit shounen-ized) way. And while it might be slightly optimistic, it has faith in the fact that as long as you make the effort, you can and will be able to build meaningful relationships with other people. Also, bonus points for understanding that different types of people exist and that not all teenagers are straight. (And for not making said teenager a caricature or the butt of a joke.)
I'm an absolute sucker for stories about youthful earnestness, and Hoshino, Me wo Tsubutte. is definitely one of the better ones I've had the pleasure to read.