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I want to customize SharePoint more to remove Recycling Bin and Edit links from the SharePoint site. Is it best practice to Copy/Paste (Create new) copy of the seattle.master page then rename it and when I am done customizing it, you right click "set as default master page" and "set as custom master page" in SharePoint Designer? I just want to follow best practices.

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I don't think much has changed so I'll provide my understanding of things.

Creating custom master pages is still possible, but not ideal, specially if you are working in a cloud ecosystem, where changes can be pushed at any time, and you would not get them.

Small customizations like those you mention can be achieved by a simple CSS (AlternateCSSUrl) or JS file (CustomActions)

If you are aware of the pros and cons of creating and customizing your own master page, then by all means, grab a copy of the default (last time I checked you had to copy the html, not the .master file) and start working.

Further reading,

To brand or not to brand, that is the SharePoint Online Question

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Custom Master pages are supported but not recommended. As Office 365 moves forward, they will be deploying new features and with an updated framework (Modern versus the Classic Experience). They are saying that if your Master Page is customized, you may not receive all current updates.

They are recommending branding using CSS and Client Site JavaScript with can be injected into your site: Customize your SharePoint Site UI by using JavaScript. This Channel 9 video has an example using Visual Studio 2015 which seemed a bit like overkill to me.

You could use the script "Scenario1" from this GitHub example along with the great aspx page from johnnliu on GitHub and get the same result without all the fuss.

Good luck!

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