The minrole feature is supposedly supported, but is not reflecting such.
[SOLVED] - Thanks to Trevor Seward
I had intentionally installed the Foundation Web Application on the WFE and not the APP, thinking it was correct since the APP should not serve pages, but apparently there are situations and reasons that it is needed on the APP server.
I followed https://sharepointumar.wordpress.com/2013/10/11/restart-microsoft-sharepoint-foundation-web-application-service-stuck-at-stopping/comment-page-1/#comment-146 to provision the service and then the missing web applications.
The Provision() method can be invoked to only provision on the server that invoked it, instead of needing to use ProvisionGlobally().