First, seems that you are directly using the template - classic as you custom template.

Please stop that, leave the classic and template_default and keep them alone.
Instead, you can create one for your own, by download a template from the download area, copy or clone a template, or create one for yourself. The best is to choose the templates which based on the new design of template_default.

Then put your own template in a new directory and modify it. Please refer to other thread related to this subject.

For the problem of your logo, first have a concept for this is better.

The logo image should not be in the full width of the page. Since there both have another elements although sometimes you can't see them.

The width of the logo should be less than:
(the maximum width for the logo) = (the full width of main page) - (all the widths of other elements)

And for matching, you can set a background color and/or background image to cover the whole areas behind the header and logo.

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