Marshalls question is a good one so Im going to update here on what can be looked at.

The DOT-NET RFID SDK (HOST-BASED) for FX-Series readers - has two sample projects 

Typically found in the Windows Program Files folder under "\Zebra RFID FXSeries Host .NET SDK\Samples\C#"
"CS_RFID3_Host_Sample1" and "CS_RFID3_Host_Sample2"  

Its "CS_RFID3_Host_Sample2" project we are interested in.
In this app - under the "Operations" menu - is "Antenna Info..." dialog.
This dialog allows for an "Array" of active antennas usable in operations.

(Indirectly - this passes a list of "Antenna's we want" for a given operation.)  See the "AntennaInfoForm" files for this dialog.
This is a lightweight Host-Based "Runtime" operation and does not change the configuration of the reader that would be saved to the reader per-se.

Saving to the reader:
The other way is using the RM operation for "Read Points" (These are the ports on the Reader) Where you can enable / disable these.

RM requires the App to Login to the reader to have RM permissions to make changes.  

Thanks again Sean. Apologies ... this was posted before the support case but appreciate your follow up!

Thank you

Marshall