I don't know why this is only sticking out to me as a topic now, possibly because I am in the habit of disabling any File Type Associations I don't want as part of the application at install time or as a first run configuration task during the sequencing steps. Maybe it didn't seem like too much of a nuisance to me, so I gave it a pass. But recently, I've had to disable File Type Associations in some crappy installs, which did not allow me to disable as part of the install or configuration options.
The possible issue? You might notice when you sequence your application. You go to Shortcuts and FTAs in the sequencer and remove the File Type Associations you don't want...You go and deploy the application and those damn, dirty File Type Associations have taken over. I believe this is down to the fact that fundamentally, the way App-V works has completely changed. During sequencing it detects certain extensions such as icons, fonts and file type associations during sequencing and points to these in the configuration file. So removing the FTA's from the Sequencer GUI doesn't have the desired effect. Personally, I think this is something that should be fixed BUT don't worry, there's a pretty easy workaround.
You can just open up your App-V packages configuration file, navigate to the File Type Associations and either remove the FTAs that you specifically do not want or if you don't want any of them, you could just change the setting to false. If you use the User or Deployment Configuration files you will need to ensure these are used when publishing the application, otherwise the default will be used which will take precedence.