Both are OK to use, as they will get you to the same place. However, due to the differences you pointed out I don't suggest using both as some do. It's best to use one or the other to update you. Though, as you have noticed the PEQ SVN does have some added tables and such because that's what the project is, the database. The EQEmu code will only provide you with core updates and none of the fancy extras I often add.
AAs are in the system tables, not the player tables which is why you won't see them as updates. Those changes are already in the big gz file. If you look in the player_tables folder the update files will only effect those tables listed there, all other updates will already be in the content gz.
The difference in version number is simply due to the way that I update the DB SVN. I give the DB and any update file (if one is needed) the current version number of EQEmu when it is uploaded, not when the change was made. So, if you see the DB SVN has a higher version number than the last time changes were required for the EQEmu code, then you are safe in that you'll have all those updates.
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