New Units: Land-based Troop Transports

there should be digging units-units that do nothing but make tunnels.  these units would have no attack or defense, and only 1 could be sent out at a time. there would be basic and advanced types, and some races would have better tunnelers than others.

HM, I haven't played it either but I could draw my imagination from playing Heroes of Might and Magic series.

If you've ever played Age of Wonders, you'll have a good idea of what I'm describing here.  In that world, underground isn't just a network of tunnels with two or three entrances/exits each.  It's basically a whole new level of "world" with rivers and cities littered throughout.  Being underground only makes it a little more confining, similar to how mountain ranges would somewhat block land movement--even non-cleared areas can still be tunneled by dwarves, with those tunnels eventually collapsing if not maintained.

In such an environment, blockading entrance/exit points would require a whole lot of power, as you'd be opposing everyone in the area above and below who wish to trade or conduct warfare between levels and need that passage to do so.

Fixed access points for subterranean locations (i.e. holes, caves) or water (i.e. shoreline) makes since, but air locations shouldn't be constrained.

I think you need to consider what I said in a more literal context, as it would have to be when actually implemented as (program) logic.  Air access locations are constrained to the place you launch (your city) and the place you land.  Also, access to air is an airship-only thing, making it in ways far more constrained than the paths between various other layers.  Otherwise, air units could intercept cavalry or ships, which is taking it too far and complicates both pathfinding and battle resolution.  How do you find the interception point between two disjoint graphs, and what should a cavalry unit's attack vs airship and vice-versa be exactly?

And what about blockages?  Some should penetrate the air layer while others do not  (i.e. mountains slow land but block air, bridges block water, unbridged water blocks land, etc.).  Airships must be able to touch land only, not arbitrarily become land or water-based vessels to get around obstacles, and a clean implementation of obstacle knowledge shouldn't require checking for content in other layers but not this one.  Proper separation of concerns is aided by separation of the data in the first place.  All these issues are dealt with by operating on the concept that there are no access points for air except two special per-trip ones: where you launch, and where you land.  Save for these, you have your own disjoint graph in which you can map your path, possibly taking advantage of trade winds, avoiding storms, and even intercepting or avoiding other units already in the air.

Things get most exciting on any layer when you introduce the concept that at a unit/army level "there ain't room for the both of us."

As for ground based transport, I think it would fit in with the world to just be able to mount the whole army on horses [borrowed from your resource stockpiles].

I like this idea.  A lot.

Fixed access points for subterranean locations (i.e. holes, caves) or water (i.e. shoreline) makes since, but air locations shouldn't be constrained.