I think there is a lot of misunderstanding going on here.
I will speak in SAGE LINGO since it is the box I am most familiar with. If you are using a SAGE EAS, you program in the region (i.e. state & counties) you are assigned by your state EAS plan. If you are using one EAS box for more than one station, you have to include ALL areas required for all stations connected to that one EAS. This will probably result in you carrying more alerts than necessary on some of your stations. If you are adding an MSRP to the Sage, it connects through one of the DB9 serial ports on the back of the Sage. The Sage will give you the ability to send an alert on just one or all of the stations.
As for automatic alerting... In the Sage programming, you have the ability to set certain alerts to automatically relay on all stations or to wait for a command. I believe there is a time limit on the wait, so if it doesn't get sent in time, it will automatically send on all stations.
As for the CAP converters... they are not as complicated as many on here want to make them sound. You program it just like the EAS unit itself. You select the state and counties you want to receive alerts for. If you are using one unit for multiple stations, you program in multiple counties. That CAP programming (state & counties) has to be the same on the EAS unit itself or it will ignore the CAP converter. Then, the CAP converter will occasionally check the IPAWS and CAP servers for any alerts for the state & counties you programmed into it. If it gets an alert, it will convert the CAP data into a NOAA-ish text-to-speech voice and attach the OLD EAS access tones to it. Your OLD EAS unit will hear these tones and fire off an old-style alert.
The only hang-up I could see with an LMA station would be the paperwork end. You'll probably be required to provide your own paperwork for EAS logs. However, I would assume you could make your own copies of the EAS logs and sign them and file them. Oh, and the other stations would have to be OK with receiving alerts for your coverage area.