Hi Mark!
It's not the current .htaccess rules that might present a conflict. It's the way WordPress multisite uses domain mapping.
One of my multi-sites is bhmbizsites.com – that's the main site of the multisite. New sites are created within the network using a subdomain structure, so those sites might be: biz1.bhmbizsites.com and biz2.bhmbizsites.com.
But each of these subsites is a client site with a completely separate domain mapped to it. The domain mapping redirects the subdomain URLs to the separate domain. So the page "biz1.bhmbizsites.com/about" becomes "spiffydomain.com/about". I'm pretty sure that this is a dynamic mapping process – if I turn off domain mapping for a particular subsite, it just goes back to the regular subdomain URLs.
So if I understand what WordFence is doing in Falcon Engine correctly – flattening the directory structure – what I'm not sure about is whether Falcon Engine would do this with the subdomain URLs or with the mapped URLs. And if it's with the subdomain URLs, I'm guessing the speed increase would be offset by having to redirect to the mapped domain URL?
Anything you can tell me about how Falcon Engine might handle this?