Are total instance storage per region and Aurora Volume size separate?

The "Total storage for all DB instances is 100,000GB" according to the document, but this is a soft limit and can be requested upwards through the Service Quotas console. As you have noted, the Aurora cluster can go to a maximum size of 128TiB which is in excess of the 100,000GB per account, per region limit. The limits are per account and per supported region,but do not include snapshot backups. I recommend requesting a quota increase based on your Database requirements. (https://docs.aws.amazon.com/AmazonRDS/latest/AuroraUserGuide/CHAP_Limits.html

I'm sorry about the misinformation. "Total storage for all DB instances" is a RDS-instance-only limit that does not apply to Aurora clusters. We will correct that bit soon.

As long as you're running a recent version that supports 128 TiB, you can scale up all of your clusters to 128 TiB each, independently. No need to request a limit increase for this.