Hi Pravin,
"The user is authenticated correctly and SharePoint site opens. But the moment user launches PHA app from SharePoint...", which means siteminder has done its primary task for authenticating a user. When navigating through the app, somehow "token is lost ", which is data redirect flow problem. Siteminder agent can play a role on this, but most often is due to client side customization, check fcc forms and POST preservation settings.
You need to find out why token is lost, or which step/component triggers or is responsible for it.
BTW, this is not the same use case as original thread, you should open a new thread of discussion.
Every integration solution can have its unique problems, with varies requirements from a business team, but I can not see why SiteMinder will prevent SharePoint PHA app integration unless we know the cause of it.
Hongxu