You can override the logo() method in your theme. However, the logo content already comes as a pre-constructed HTML fragment (from qa-include/app/page.php). The logo() method only puts that fragment in a <div> tag, so you need to change the link target with a string replacement, e.g. like this:
public function logo() {
$this->output(
'<div class="qa-logo">',
preg_replace('/href=".*?"/', 'href="https://example.com/"', $this->content['logo']),
'</div>'
);
}
The .*? in the regular expression is a non-greedy match, i.e. it matches only up to the next double quote, not up to the last double quote as .* (without the question mark) would.