Here is a good read about how alternators work and what the pins are;
https://wilbo666.pbworks.com/w/page/39441708/Toyota%20Alternators#AlternatorRegulatorSTerminal
Its for Toyota so it is not exactly applicable to Subaru's but it is still good info.
Apparently Toyota alternators have an Ignition wire instead of the computer wire to turn them on and off (the alternator is off until power is supplied via the ignition wire) where as Subaru alternators are self exciting (no idea how that works) so have a computer wire that is used to switch them on and off or partially on which is controlled on more modern models by the ecu.
This control is in addition to the alternators internal voltage regulator meaning the alternator will run fine in an older vehicle and wont over charge batteries.
All the computer control does is allow the ecu to get the alternator to charge batteries at different rates based on temperature and also turn it on and off to help with starting and save fuel.
I think I may have worked out why my battery voltage is a bit low and possibly why it decreases with longer drives.
When wiring my dual battery system up I extended the lead to the fuse box. In doing this I have unknowingly extended the alternator sense wire away from the battery.
I measured the voltage in the fuse box with the engine running it sure enough is 14.4-14.5V however when the two big batteries in my car are charging, drawing heaps of current the voltage drop between the fuse box and the batteries is 0.5V or more meaning the batteries always see under 14V.
I am guessing as the engine bay heats up a bit on longer drives then the resistance of my extra wire increases causing a further decrease in voltage at the batteries.
Soon I will make my own alternator output cable directly to the start battery as well as a connection to the 'S' pin of the alternator as a direct (but separate) connection to the start battery. That way I will have maximum power and voltage available at the main battery that there is possible for there to be.
I might still look into an alternator upgrade as well because I am always paranoid that if I stall it when winching hard there will be no juice left to start the engine again and the 70A is somewhat marginal at times anyway.