As long as you tell it to remove copy protection when you rip to ISO then the burnt BD-R/RE should work fine. I have about 10 3D movies backed up to DL BD-R and so far they all work in my 3D player
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You can rip it to folder anyway you like, I just find it easier to use Anydvd HD's own option as it's always worked for me.
If you rip it directly to an ISO then you can't put back in the missing folders which then means it's not a compliant unprotected disc and PDVD can come up with 'Unsupported format' and other error messages. The guide is for FULLY COMPLIANT discs
The only 2 folders you need for a working blu-ray are the BDMV and certificate folders. All the rest you don't need. Zipfiles etc, are usualy firmware upgrades for players & stuff.