Would you be buying the ships and troops or would the activity be spawning them in for you? akblabla's Alternative Skirmish
had changing enemy LZs though much of it is pretty damn confusing (line 488 is probably the most relevant bit unless you want to try to duplicate his method of picking where the box is.
Anyway I can think of two ways to do it. The better way would be to add boxes in lua, you'd create two boxes (in lua) for the original spawn areas then you'd replace them with bigger/smaller boxes depending on how far the enemy has advanced. You'd have to determine milestones for enemy advancement so you would know when to change boxes, perhaps you could do that by making area boxes and checking enemy counts or you could just base it on how far the enemy has gotten (i.e. the farthest enemy x position).
The other way would be to create the LZs in the area editor, making each LZ its minumum size, then put a bunch of smaller area boxes in between. These smaller boxes would originally increase the size of the player LZ but when an enemy is in a box that box (and all those behind it) would then add to the enemy LZ and not to the player LZ. This would be fine except I don't know of a way to add area sizes together so as far as I know you'd have to use random chances to make the ship pick where to spawn. Though it may be possible to create a box from the beginning of the original area to the farthest captured area and use that box as the actual LZ.
In short, it's either pretty damn difficult or there's a very easy way that I'm missing. If anyone has suggestions on this I'd like to hear them too cause my ideas don't seem great. Plus I don't think either one of them would help if the player is supposed to buy his own ships.