While I don't understand the "security reasons" why one should not be able to run an executable from one's own file manager (where are we suppose to run them from? A terminal? Well, we could just as easily list/copy/move/... our files from there as well.), one certainly should be able to modify the executable flags for files from one's file manager (if this is not a "pure" file manager function, what's the point? Ever write shell scripts?). BTW, Linux executables are not "DOS font" types either.
You can set the executable bit on files where it makes sense (ELF executables, all sorts of scripts, etc), but unlike other file managers, you cannot set executable bit on audio files, video files, documents, etc, because it simply doesn't make sense. If the "Program" button is not available for such files, it usually means that your shared-mime-info installation is broken.
Resolving to INVALID then.