The merge setting pulls the page content up and under the site header, and is generally used when you want a transparent site header over an image for example. It doesn’t look like you need this so you can delete the Header Element.
Any other differences in height will be related to a the padding / margins you have set in the GenerateBlocks Containers etc.
Thank you for your answer, but this is not my problem.
It’s pretty hard to explain and I haven’t got a very good english, sorry.
For exemple, when you go from homepage to “LE VILLAGE”, the logo and even the navigation menu are not at the exact same place on both pages… And I don’t understand why. It’s only a few pexels.