Django-Pinax : How do you use a pinax app apart from what you get with a pinax base project?
You seem to be assuming that unless all of Pinax is useful, Pinax as a project isn't useful. It was never the intention that Pinax be a single thing, all of which you use on a given project.
If all you find helpful is the project layout, that's fine. Pinax suggests a standard project layout (which you can use alone with pinax-project-zero).
If all you find helpful is the pinax-project-account (django-user-accounts and a few other things, already integrated with templates following bootstrap class naming) as a starting point for you site, that's great. Pinax is fundamentally about getting you started sooner and pinax-project-account is a suitable starting point for most sites with user accounts.
Once you have a project, you are free to add any Django apps you want. There's nothing that requires you to use Pinax apps. "So", you ask, "why does Pinax even bother having apps?". 
Well, because apps aren't isolated. Reusability isn't just at the level of app but also groups of apps. Take, for example, a waiting list app, an invitations app, a referral code app, a points app, a badges app. Sure these can be developed and used independently.
But if they are developed with the same mind set you can make sure the waiting list app and invitations app and referral code app work well with the user account app (and don't duplicate anything). You can make sure the referral code app plays nicely with the points app and the points app plays nicely with the badges app. You can make sure your forum app doesn't try to do something your moderation app already provides. Or that each app isn't trying to solve avatars its own way.
So Pinax isn't trying to be a "directory" of apps. It's a family of apps, themes and starter projects written with each other in mind.
I am trying to understand Pinax and plan to use it in my next project.
I have started with a pinax basic project, and now I have something to go with runserver.
Now, I understand that I can customize the initial setup that I got from pinax and customize the profiles, themes, etc as per my requirements.
But is that all that pinax provides ?
I am very confused here, like I want to use the pinax phileo app in my project, so how does pinax helps me do that ?
My Effort :

I searched and found that I have to install it with pip install phileo
Then, add it to INSTALLED_APPS and use it as required.

But what did pinax do in this ?
Pinax has phileo featured on its website, but why ? Since I could have used it just like any other app on my non-pinax django project.
So, my question in a nutshell is :
What does pinax provide after a base project and default templates that come with pinax ?
Right, now it feels like pinax just provides a base project with some apps already working with some default templates. [ That's it ? ]
Then, what about other apps featured on pinax's website that do not come with base projects ?
Please, help clear up the confusion !
Update
My question is somewhat - What is the significance of pinax-ecosystem when we already have them listed somewhere like djangopackages.com ?