What's the 3 domains limitation?
Netsparker Standard can only scan 3 domains that you chose, while buying a license or right after you buy it you should supply us 3 domains. You won't be able to change these domains until your license expires. If you need to scan more domains you can either buy a new Netsparker Standard Edition license for an additional 3 domains or you can upgrade to Netsparker Professional to scan unlimited domains.
Can I upgrade it to Netsparker Professional later on?
Yes, you can.
How to choose 3 Domains to Scan? What's a domain?
Standard License can scan only 3 FQDNs, if you want you can give only one or two FQDNs to start your Standard License and add other domains later on.
As you can see shop.example.com and example.com are separately counted.
Although by default all standard licenses include: