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I post it here as I think it is a Panels issue.
I got a D7 website whose pages are rendered through Panels, actually Node, Taxonomy Term and User templates. I haven't added node:content pane to the panels as the main content. Instead I put a collection of views in the different regions of my panel layout.
I installed Remove Generator and set up Meta tags, OpenGraph Meta tags and Schema.org for my node types. But it seems there are no meta nor Schema.org information on pages displayed through Panels. Nor the Generator Meta is removed in them.
I'm sure it is up to Panels as a collection of views and panes since the problem disappears whenever I disable the Panel template or I put the node:content pane in it.