I was going by how this site works and how other sites on the web work. So I thought the intention of the index.php file was more of a portal to use with IP.contnet then a file to show the default page of the Ip.content. It was not until you just now explained it that way that what you are saying is less confusing. However I still would much rather it be a portal page then show the default Ip.content page.
All the index.php file is intended to do is allow you to show the IP.Content pages outside of the forums. That is it's sole intention. So, when you first visit it (at domain.com for example), it loads your default page.
The index.php?app=ccs URL ALSO has to show the default page. What else would it show?
Going by your example, none of the other applications show you two different default pages. This is hard to understand, perhaps, because none of the other apps also let you show the pages outside of the forums, but it's not like /index.php?app=gallery and /gallery show you two different pages, do they? This is the same idea.
Any way that is why I did not think it was consistent with the rest of the apps as I was looking at it as a completely different app all together. So to give you a better idea of how I was looking at it. If the gallery worked like Ip.content at least the way I was viewing it. If you installed the Gallery you would then no longer be able to get to the forum or at least not have an easy way to get to it as every time you pulled up the forum it would go to the gallery. It does not however work that way so I was confused as to why Ip.content worked that way.
This site (invisionpower.com) should be a better example of how the software works. I mean I did find out you have 2 installs of the forum and Ip.content to get the site to work the way I was thinking it worked. I do not want to have to have 2 installs to get my site to work the way this one does. Honestly though if Ip.content did work the way I want this site could go to just having one install instead of 2.
So basically my idea is to change the purpose of index.php to show what ever page the user wants. That way they can make it show the Ip.content default page or have it show a portal like page.
Also you examples do not exactly match with how I was thinking Ip.content worked, but does give me a better idea of what you intended it to do. A better example is the gallery one I gave above. Another one would be and probably the best example would be the Ip.portal. If the ip.portal worked the way the index.php file worked then all it would do is pull up the forum however it does not so in my thinking Ip.content does not follow the rules of the other apps.