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Enable custom logo upload if logo is not in header

If I read your question well, you already use WordPress Custom Logo, but you want a different logo on your front page. This means you will need to upload a separate image.

Assuming you already know how to use the customizer in general you will need to build an upload field like this:

$wp_customize->add_control( 
    new WP_Customize_Upload_Control( 
    $wp_customize, 
    'wpse238690_front_logo', 
    array(
        'label'       => __( 'First image', 'wpse215632_theme' ),
        'description' => __( 'More about first image', 'wpse215632_theme' ),
        'section'     => 'wpse238690__section_id',
        'settings'    => 'wpse238690__setting_id',
    ) ) 
);

Replace the section and setting to fit the control in the right place in your customizer system.

In your header template you must then include a conditional with is_front_page: display the normal logo in the header if you’re not on the front page. In your front page template include the logo with get_mod('wpse238690_front_logo').

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