Really? I can't stand the custom CSS, feels like every sub Reddit is a unique website. I've had custom CSS disabled for as long as I've used CSS, I thought it was a terrible idea.
The CSS customization really does work wonders for things like sports-related subreddits or national sub-reddits, where you can attach your hometown/county to your profile name, so that everybody can make fun of you and you can make fun or everybody else (the same goes for /r/europe).
I also found CSS customization extremely valuable for the /r/syriancivilwar subreddit, where users can attach the flag of a certain faction from that war to their username: Government, Al-Nusra (or whatever they're called now), the Kurds etc. At some point a couple of years ago there were several users who had the ISIS flag attached to their username. That was an excellent way of knowing where the other party was coming from when writing down their comments.
https://www.reddit.com/r/modnews/comments/6auyq9/reddit_is_p...
They're going to work with mods and make sure CSS still works.