There are caveats, and what you've pointed out about the Utility itself being updated is one of them. Problem is that some things can't be fixed as long as the volume is mounted.
I've always sworn by DiskWarrior for such tasks in the past (and still do), but some people have impressed upon me not to underestimate the capabilties of Apple's own utilities. Even where an OS would change (ie: 10.4.9 to 10.4.10), DiskWarrior is still v. 4.0 itself, so using a third-party utility under such circumstances raises the same questions that using Apples Disk Utility would for the same purpose.
Repair Permission is only one part of the Apple Disk Utility. Where running from the volume or install disks might be weighed, cm is onto something with his statement that permissions shouldn't change. But we also have docs and tech notes to refer to before doing maintenance when we're unsure.
The other parts of the Apple Disk Utility include Verify Disk and Repair Disk. In some cases a mounted disk cannot be repaired. There's really no choice but to try to repair from a CD-ROM (or DVD-ROM)-- either from Apple or from a third-party.
In those cases where one might be concerned if their third-party utility is no more up to date than their Apple install discs, then there is the *ugly* option of buying the latest version of OSX discs from Apple even if you already own an earlier version of discs.
When in doubt, contact Apple Tech Support directly. Apple's docs are quite informative, but they also include "safe" statements that don't always address all concerns on a given topic. How the Disk Utility from 10.4.3 discs, for example, impact on permissions or general volume repair on a 10.4.9 volume is something only Apple could answer as per your specific needs.