Here is the thing you are doing wrong, Set the Hydrogen - Default to be Default Template, I removed assignments from all other styles.
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Now go to the Hydrogen Gantry 5 Admin and in the Home outline, you need to set the Assignment to Home Menu item.
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Now you need to adjust the Base outline Layout and set what you want to appear trugh out the site, Menu footer etc ... and then in other outlines you simply inherit that in layout so you dont need to alter that on each outline.
docs.gantry.org/gantry5/configure/inheritance
Let me know if its clear to you?