We are using SharePoint 2016 along with Nintex 2016.
Our custom master page is applied to all SharePoint page except Nintex Workflow designer page.
So how to change the master page of Nintex Workflow Designer??
I am not sure it would be a wise idea to try to get your master page working on the forms designer page. It is not a recommended practice to customize these types of system pages in SharePoint. Your master page should be considered for your main parts of your UI and its recommended to use seattle.master system master pages. If Nintex changes something in there designer you could be in danger of be unsupported or breaking because of the change.