Dumping games FAQ? Technical overview of each step?

I've begun dumping my games and have run into a few questions that--at first glance--don't appear to be addressed via the FAQ or quickstart guide...

I can't believe there isn't more discussion about how to rip discs.  

Here's what I've learned--at least with BCUS98174-[LAST_OF_US].

Imgburn rips it in half the time IsoBuster does.  The .iso CRCs match down to SHA-1.  They're identical.

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I patch the .iso with the corresponding IRD.  The game version, app version and update version all match the IRD.

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I decrypted the .iso, then extracted it to folders.  The decoded folders fail a check using PS3-ISO-Rebulider (ignore the two unnecessary files--they were .par files I generated).  The vast majority of my rips pass.

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I then FTP the entire contents of the Last of Us to a local folder.  It fails in exactly the same manner.

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I then used Multipar to index each individual file of the decrypted Imgburn-based folder structure.  I verfied it.

Then I copied those .par files over to the FTP-derived folder structure and ran a verify.

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The files--each and every one of them--are identical.

So even though my rip fails the IRD check, it is identical to an FTP-derived copy, which has to be correct--no?

This makes me believe that IRDs only work as a guide to which sectors are encrypted.  My retail copy of The Last of Us differs from the one that the IRD was made from.  If it was file-by-file, then I would have files that failed a comparison between the non-matching IRD and the FTP copy.

So did I just get lucky with The Last of Us, or can I proceed to save wear-and-tear on my CFW PS3 by ripping via pc blu-ray drive, and ignoring any mis-matches with the IRD?