As to the compile flags, if you just keep it simple like this:
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./configure --prefix=/home/compguygene/aa --enable-dedicated --enable-armathentication
The --enable-dedicated is really the only flag you need to set the flags appropriate to build the dedicated server. The --prefix=/whatever-this-directory-is/armagetronad-version will cause the proper files to go into the directory structure that you have identified. Commands like --disable-etc would be used in a more granular way, though I am not exactly certain how as I have never used it.
You can use the script on the wiki page you referenced to have a custom ai. I used the same script myself to host your old servers with custom ai's and others with different ai's. You just have to make one change.
The following line is from the srv script which actually starts the server
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$tron --resourcedir $resourcedir --userconfigdir $userconfigdir --vardir $vardir
You need to add the --userdatadir parameter to the command to specify where to find things like custom languages and your own aiplayers.cfg.
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$tron --resourcedir $resourcedir --userconfigdir $userconfigdir --vardir $vardir --userdatadir /whatever-this-directory-is/armagetronad-version/servers/"$1"/
This will create a directory called resource under the servers/server-1 directory. That is where the aiplayers.cfg file will go.
All of this, by the way assumes that you are using .2.8.x servers. .4 servers are similar, but no longer use the var directory and put everything in that resource directory. So, watch for that as you experiment, things might be different in a new .4 build. I would take the time to verify this behavior better for you, but I let my old vps expire as I was unsatisfied with its performance and I will be getting a new one very soon, just not yet.