Hey there Alex,
Does this mean there's one more feature I still haven't paid? Is the custom design upgrade not included in this automatic renewal?
That's correct. There is a WordPress upgrade called Premium which includes both the domain upgrades and custom design (among a few other things), but it looks like you purchased the upgrades separately.
The good news is that any CSS changes you made should be preserved and reappear when you re-add the customization upgrade. You can do that by heading to Dashboard>Store and purchasing the Custom Design upgrade for $30.
Pro Tip: Once purchased, head to Dashboard>Store>My Upgrades to enable auto renew for Custom Design or any of your upgrades so you don't have to worry about them expire :)
Hope that helps! Let me know if you have anymore questions!