As I understood from the spec, the primary/secondary Mothership IS the command station. When mothership warps out no other big targets left on the planet so AI may be busy for a while with maybe unpowered defences (Mothership had the power), but ultimately should jump through, and most likely it will jump through the nearest wormhole.
And when AI leave through one wormhole, another Mothership warps in through other wormhole which will automatically start repair cycle (no engineers now).
If AI will not chase (will divide forces equally between all wormholes) this means that in case of a big number of wormholes the AI forces got very diluted.
If Mothership is not unbearably slow, then a few forcefields may provide needed time delays.