The concept is that you should be giving each of your users (or system components) their own database for only their data, rather than having one huge database everyone's combined data is stored in. It's about changing the way you think about the data storage in your application. Understandably the 10GB limit sounds small, but in reality it is a lot of space for a database. You can fit millions of records into it while remaining under the limit. My biggest db for example has 15 million records across 200 tables, and is just over 2.5 GB.
No, it's not possible at the moment. There is an ATTACH command in sqlite which can load in more databases but D1 hasn't implemented it, and I doubt they'll add it