Can 2 DKP lists be created under one website? For instance, I currently have a 10-person raid DKP list, but now I want to make one specifically for a 25-person raid starting from scratch and independant from my 10-person raid list.

Yup. Just make a new DKP System. The admin of the site might need to be the one to do it if your security isn't high enough, but it's a matter of clicking the "Create New DKP System" link on the admin menu.