I think you're right about all that, except it's the implementation they drew up for bidirectional site to site! But yeah, feels a little kludged together..VPNFusion is probably only designed to shift internet connection through various internet clients. I dont think you could use it for server peers and for site-2-site it obviously work but with limitations. I.e you cant simultaneously connect to other lan and internet via a 3rd vpn, the site-2-site is blocking other vpn/connection capability. But the more complex any function gets, the harder it will be to use.
But the bottom line is that it works for you and thats all that matters.