Seeing as most legacy browsers do not support different variations of CSS, the CSS you've applied to your header and footer will be stripped out. Instead, custom CSS can be configured separately through your control panel. Administrators will see the legacy browser CSS at the bottom of their Custom Site CSS page.
You can then use this to apply any legacy browser specific CSS in order to brand your site for your legacy browser experience. If you're unsure about whether certain types of CSS are used, caniuse.com is a great resource which will inform you of supported CSS properties on legacy browsers.