Auto Generated HTML source code formatting

I know it’s really trivial

Yes. Yes it is.

…we are shooting to do the best job possible

Spending any time whatsoever on fixing tab indentation in your output HTML as opposed to focusing on the quality of your source code is not doing “the best job possible”. You should be minifying your HTML on-the-fly anyway!

But for the sake of answering a question, you could use the style_loader_tag and script_loader_tag filters:

function wpse_248549_tag_indent( $tag ) {
     return "\t\t$tag";
}

add_filter( 'style_loader_tag',  'wpse_248549_tag_indent' );
add_filter( 'script_loader_tag', 'wpse_248549_tag_indent' );

However, this won’t handle other output that might be attached to wp_head – you’ll either have to use the same approach for other hooks (if available), or you could use a dirty bit of output buffering:

add_action( 'wp_footer', 'get_in_line::open', 1    );
add_action( 'wp_footer', 'get_in_line::stop', 1000 );
add_action( 'wp_head',   'get_in_line::open', 1    );
add_action( 'wp_head',   'get_in_line::stop', 1000 );

class get_in_line {
    /**
     * Start the output buffer.
     */
    static function open() {
        ob_start();
    }

    /**
     * Get the contents of the buffer and spring clean.
     */
    static function stop() {
        $lines = [];

        foreach ( preg_split( '/[\n\r]+/', ob_get_clean() ) as $line ) {
            if ( trim( $line ) !== '' ) {
                if ( strpos( $_line = ltrim( $line ), '<' ) !== 0 ) {
                    $_line = $line;
                }

                $lines[] = $_line;
            }
        }

        echo "\t\t" . implode( "\n\t\t", $lines ) . "\n";
    }
}