Yes, Portlet Factory has always fully supported non-Portal applications for WebSphere Application Server. This is a fully supported environment.
Websphere Application Server Community Edition (WAS CE) and Tomcat are supported for development purposes only.
When working with a non-Portal application server, the generated WAR file uses the servlet interface for application execution.
In general, any model can run both as both portlet or standalone (non-Portal), and a single project can automatically generate both types of WAR file. When running standalone, some Portal-specific features such as Cooperative Portlet (Property Broker) cannot be used. However, there are often alternate mechanisms that can be used in non-Portal scenarios. For example, Portlet Factory events can be used for inter-model communication in both Portal and non-Portal environments. For creating applications that display multiple models in non-Portal scenarios, the Model Container builder can be used to build container models that display additional models.