@AndySylvester I have no insight into what's going on behind the scenes, but I do see your plugin.json file is missing a semicolon at the end of line 4. Micro.blog is probably choking on that and that's why your plug-in won't update.
When you make changes via Design → Edit Custom Themes they will be reflected right away because you're circumventing GitHub altogether. But the changes are local to your account. Other users who installed the plug-in won't see the changes you make there.