I see now on your site the Join NPN button on header is custom button and the Sign In button use Discourse Connect. Guest Gate modal works as expected because you use Discourse Connect login so the signup button is not appear by default. It is hard because users who use Connect cannot use guest gate custom urls settings for authenticate login because that url is mostly generated. But it seems to Memberful login url is not contains generated section.
I think we should make separate settings for Discourse Connect usage. 
I will add a setting to add sign up button to Discourse Connect.