Apps lacking of file extension registration and some other strange behavior

Hello,
I noticed that some apps which I installed doesn't add context menu entries like there non-portable counterpart would do so I'm asking if there is a way to get those entries in a simple way, e.g. Notepad++ would add "Edit with Notepad++" to the context menu.

Edit1: Alright, this is intended behavior. But what is meant with:

During use, a portable app is permitted to modify registry entries and files on the local drive, however the registry and local files must be returned to their pre-run state on exit. This may involve backing up and then restoring the settings for a local copy (in either the registry or APPDATA) of an application on start and exit. The portable app must continue to work (settings and preferences maintained, language selection maintained) as the drive letter changes as the device is moved between computers. The applications Most Recently Used (MRU) file list should continue working as well.

It's from point 6. Host PC Modifications & Portability in PortableApps.com Format™ 3.5

I also noticed that Notepad++ (in admin mode) is not able to register the file extensions I selected. Bug?

All apps are started via a portable.exe, e.g. Notepad++Portable.exe which in turn starts the original.exe in the app folder. Whats the different between starting the one over the other?

There is another strange behavior: When I pin an app to the task bar it always shows the SpashScreen although it's disabled. Same behavior when I start them as administrator from the menu. Bug?