Of course, you're absolutely right. Some people repair, or recommend repairing permissions for situations where it isn't appropriate. Repairing permissions only addresses very specific issues. It is not a "cure all" or a general performance enhancer, and doesn't need to be done on a regular basis. It also doesn't address permissions problems with your files or 3rd party apps.Most evidence suggests that Disk Utility's Repair Permissions does NOT do ANYTHING for third-party installed software.
Disk Utility repairs the permissions for files installed by the Mac OS X Installer, Software Update, or an Apple software installer. It doesnt repair permissions for your documents, your home folder, and third-party applications. You can verify or repair permissions only on a disk with Mac OS X installed.
If repairing permissions results in error messages, some of these messages can be ignored and should be no cause for concern.Does Disk Utility check permissions on all files? Files that aren't installed as part of an Apple-originated installer package are not listed in a receipt and therefore are not checked. For example, if you install an application using a non-Apple installer application, or by copying it from a disk image, network volume, or other disk instead of installing it via Installer, a receipt file isn't created. This is expected. Some applications are designed to be installed in one of those ways. Also, certain files whose permissions can be changed during normal usage without affecting their function are intentionally not checked.