I brought them up not because I think they need reimplemented, but because those mechanics were there to solve certain problems. If those problems need to be solved in AIW2, and if those solutions come in the form of new mechanics, then those mechanics need to be in the design doc, even if they're not the same mechanics.
Well, that and just for the sake of completeness; Chris did ask for every single mechanic in AIW1.
I would be much happier if transports just refused to go more than X hops out, rather than attritioning, assuming they return at all. I'm not sure how the currently planned 'fuel is like energy except you have a separate pool for mobile units' system solves the transport issue; did that change again?
I think DG Lairs and any other build point-based units will work really well as ship bays, actually. A DG lair could be nicely implemented as a ship bay that contains 3 dire guardians, and periodically builds and releases dire guardians when alerted. That's basically how it works today, except the ship bay version lets you see what's going to spawn. You'd still need a way to say 'this ship bay doesn't get reinforcements but instead builds X when alerted', ideally in XML for the modders, and perhaps specified in time units rather than build points for clarity. I think Preservation Wardens and Roaming Enclaves and Neinzul Nests use a vaguely similar system, as well. I don't think these need to be implemented very differently under the hood, they just need a better UI that shows what they've built and how long you have until they build more.