Moving the nether is valid too. The largest drive I saw was 128x128x128, four quarries worth of nether!
I can easily see having an area set up just large than a quarry with permanent spacial pylons oustide of it, have it on its own ae network (subnetwork) and just imput a full drive from the nether, quarry reset and you are good to go. You may be able to automate the setup and teardown of the spatial pylons in the nether with turtles. Just remember that entities are saved as well as blocks, including zombie pigmen, magma cubes, and ghasts! I don't really want to let a ghast loose in the overworld or mystcraft dimention near my base.