Yes it is's SEO the same here.
However it looks like the only difference is that in my case I do not see any error when I turn on/off the plugin. Just the rel author is missing in the homepage.
I have added the following manually while waiting for the support:
<?php if ( is_home() ) { ?>
<!-- for yoast's support - I have added this manually, because the plugin is not adding it - please help -->
<link rel="author" href="https://plus.google.com/XXX" />
<?php } else { ?>
<?php
}
?>