I am unsure how I feel about automated systems to be honest.
How would you control these mining rigs ? You have to be close by or can these be done remotely from a different star system ?
It actually balances pretty well out of the box I think. They are 'automated' mining rigs - your function is to find somewhere to put them, and put them there. They then mine, at a predetermined rate, and fill up their storage capacity with whatever minerals are abundant on the planet you placed them on (basically, the further you go away from the core systems, the more valuable the returns in FE2). When they are full, they stop mining.
The only 'control' you have over them is dropping them, picking them up, and emptying them when full. All of this requires you to be landed within the vicinity of them.
In a multiplayer environment, it could work well quite simply. These things do not broadcast their presence (the owner logs the coordinates in his ships computer, no need for a beacon). You could scan for them at a limited range however, giving thieves a reason to be cruising over planet surfaces on the 'off chance' of getting a signal from one.
I would simply have it that a rig is coded to the owning ships ID; if another ship tries to empty it - nothing prevents that, but the rig does send a message to its owner. If you made it so that it took a minute to load a tonne of goods from one (if you were not the owner), that gives the owner 20 minutes (on a 20t rig) to chase across the galaxy to respond to a potential thief (who may or may not have left the area by the time the person arrives).
If the owner is offline; their rigs should not be visible to anyone and not generate any resources for the owner - to prevent going on holiday and coming back to find someone destroyed your mining empire.
Opportunities abound for different rigs to mine at different rates, but faster ones would be bigger and detectable at greater distances.
Emergent gameplay would involve thieves who just try to find multiple rigs, taking 2 or 3t on material from each one so that they could escape before the owner can return, right through to pirates who will deliberately set off the 'alarm' and then go and hide, waiting for the owner to come back to check on their equipment.