SEO is not about your homepage. Actually every homepage is the worst page of any website in terms of SEO.
I’ve been using the following strategy and everything works great for me:
I have a WordPress installation in my main domain
I have an SSL installed (Free from Let’s Encrypt does the job) there
I use the ClickFunnels WP Plugin
I share my funnels with or without the plugin depending on what I want to do
I have a tab in the main site where I have the Blog section with my SEO optimized articles
In short, SEO is not about the meta tags and keywords.
It’s a series of things when you deal with (on page) SEO like The url, the headline, the subheadlines, the content itself, the keywords/phrases/longtail within the article and much, much more. These are just a few.
Yoast SEO WordPress Plugin helps lot for basic on page SEO. There is also the off page SEO which in essence is backlinks to your site and is a whole new story.
So to wrap up:
ClickFunnels is not SEO friendly, it’s awesome to build funnels. SEO is not about keywords and meta tags and page title that CF gives you. You CAN optimize your articles within ClickFunnels but it’s easier in WP. Your homepage is never optimized for SEO, your articles are (if you have any)