Most of those tables a should be related to the login server and if you do not run your own, then it is not relevant.
The dump is different because it truly is a dump of the PEQ database minus the character tables. The original DB source was a much more manual process to retrieve cleaned tables and create a new DB file that was exported.
In general the process has not changed. Source in the initial DB and then source in changes from the github folder as need. If you to source in from old stuff, then you will have to look into manually checking things..
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