That is not very good.
Suppose you create an audio file with Audacity and a series of images with ImageMagick and GIMP, then use ffmpeg to combine them into a video and VLC to view it. They're all operating on the same files.
What we need is to add an application list to filesystem ACLs and then have security groups like Video and Finances which contain apps. Because GIMP should be able to access your photos but not your accounting spreadsheet.
It should even be possible to do some of this automatically by file type, e.g. GIMP can access any PNG file the user can but not any spreadsheet file, or read a shared library but not write to it.