Is there a reason we have a 500 character limit inside section Custom CSS? Can this be increased, or better yet, removed?
I dont think the Custom CSS section is ment to be used for anything else than small merchant-focused changes. Or better yet, temporal changes. It’s not very good practice.
What’s the usecase for having so much CSS in that field? 
Sorry to revive the old thread.
The use case is to avoid theme code edits to allow theme to auto update.
Living with “Custom CSS” only (and “Custom Liquid”) will allow theme to autoupdate.
Then, the beauty of CSS scoped to particular section without the need to invent or update selectors manually. No worries about section being duplicated, removed and re-added, etc..
It’s ok’ish to add your own stylesheets if you have a contract with customer to support and update their theme. Even then, you’re probably charging for these updates.
While I understand that removing the limit may lead to people loading tens and hundreds of kilobytes of CSS (like it was with metafields), the 500 bytes is too low IMO.