I've had a similar scenario with Yoast - re: adding the site name (in this case, site URL) to the title automatically, but not really registering that fact when you use the plug-in on each page/post.
If it were me, I'd advise against 2, because you're right, it does look kind of redundant & spammy. OR, if you want, you can turn the setting off that automatically adds the site name at the end of every single one of your titles, and then just add it manually so that Yoast does register it. In WP, these settings can be found in the Titles & Metas section of your Yoast SEO plugin (accessible from the menu on the left, right under SEO's dashboard).
I hope that helps!