While I agree with you that KINKY BOOTS didn't need to be a treatise on sexuality (or gender identity, for that matter), I think it would have been possible to give the Lola character a story on par with Charlie's story. The show as it was written is almost exclusively Charlie's story and Lola is a flashy featured role in that story, just as the other characters are. But Billy Porter is a STAR and elevated the role to another level that is probably not at all on the page.
How great would it have been to watch Lola function in a story that had nothing to do with Charlie. Maybe Lola and Don could even have evolved into something more.