I want to use my custom masterpage as a site masterpage and keep the default "seattle" masterpage in the settings view ("System master page option").
Is this possible?
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You have 3 options:
If you open a page in SharePoint Designer you can see a MasterPageFile setting which can be modified:
Additionally you can also set this through the UI, by navigating to the Site Collection Settings --> Look and Feel --> Master Page. Here you can choose the Site and System Master page separately.
Also, this can be done through Powershell,
I have posted that earlier here Apply master page to the settings page