One problem I have with Acromyrmex, is they get their fungus pellets stuck in the cotton and end up destroying them. I'm not positive that that is the reason they end up destroyed, but I am positive they get them stuck in the cotton as well as their mandibles (all ants seem to have this happen sometimes), and it sure looks like this contributes to the destruction of their pellets. I think this idea might work really good for this species.
I think all together this is a great idea, and would even eliminate the need for an actual test tube with a sealed end (for vacuum/air pressure purposes), however, the one problem I do see, is moving the colony to a new setup would probably require waiting for them to move themselves, which I rarely do. If they've dug into the agar, you're probably not going to be shaking them out. Again, for Acromyrmex this is still the perfect solution, since due to the fungus garden, I would never be shaking them out of their test tube anyways. Since I don't have any new Acromyrmex queens with their fungus pellets at this point, I probably won't be trying this for them until next year if I end up catching some more.