@rmsilver7 For multisite, please install this plugin on Network Admin site only. If you use subdomains it’ll work with wildcard SSL.
If your control panel is cPanel: ‘Auto-Install Free SSL’ fetchs all the domains information (document root etc) from the cPanel API. Getting the document root is required for domain validation with Let’s Encrypt. But the domain mapping plugin doesn’t cordinate with cPanel. So it’ll not work. You can try adding the domains in the cPanel as add-on domains. But I don’t know if it can conflict with the domain mapping plugin.
If your control panel is NOT cPanel: Please try adding the domain information (document root etc) in ‘Auto-Install Free SSL’. It should work. But still I am not 100% sure.
In either cases you may give a try and let me know how it goes.