Yes. If you want two entirely separate websites, you will need two Web Site Setup records, which will require two SCS or SCA licenses.
You can do it with a single Web Site Setup record, but both websites will share the same setup record. When 2020.1 is installed, it will not overwrite the Elbrus bundle, and it will create separate SSP applications from the SSP applications used with Elbrus. When deploying the SSP applications, link to the domain not to the site. There are probably other steps to get two websites to work on a single web site setup record.