Hey Hordecall, first of all thanks for your donation! About your problem, I assume you've already tried changing the base color of the theme? This also affects the tile palette background somewhat (if you're on macOS, change to "Tiled Fusion" theme first). Another option is to try a development build where I've coded a background color option per-tileset, though unfortunately it's a little unstable at the moment. You can find the latest build for Windows here.
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That is not a glitch but an unfortunate inconsistency in where the objects are anchored. Whereas rectangle objects have their origin in the top-left, the tile objects have their origin in the bottom-left (or even bottom-center, in the case of isometric maps). At some point in the future I'd like to unify all this.
I think it doesn't really matter whether it's on GitHub, Bitbucket or GitLab. They're all great services. GitHub is the biggest, but GitLab allows you to log in with accounts at either of the others as well as with Twitter or Google.
In any case that's great news and I'm looking forward to trying it out!
You could just put a disclaimer along with the code that you're not comfortable with it. Besides, maybe somebody would like to help you clean it up! I would definitely like to try out your tool, but I don't like running applications that hide their source code. Also, I'm generally working on Linux.