it seems relatively trivial to maintain parallel route-maps for such as aerial, aquatic, magma-surviving, etc, as well as a "pet map" that handles pet-forbidden doors as non-routable
Trivial yes, but memory hungry if a trivial method is used. As you mention they might be better ways to store the 5 (or more) fold data.
What I also meant to mention is that a bit-wise "passable/not-passable" flag was made, that had not been given any form of compressive optimisation (by programmer or compiler) and was inhabiting an entire byte regardless of only being true/false, then a number of different flags could be loaded into the same byte of storage to
no extra memory usage (and trivial logic applied to the setting/retrieval of the state). But I still err towards zone-trees optimised towards differing requirements.
A possibility would be that each zone was either passable or not (ie: no zone could have both a passable and a shorter but non-passable route) so zone calculations would have to generate two zones where there was two adjacent routes, one with was all open, one which was not passable by a subgroup. Then the path finding could just treat non-passable as inf cost if that critter cannot pass that way. Not perfect, but fairly simple.
This reminds me of the vectorised world I have breifly aluded to. Surface-to-surface convex polyhedra, the sides being indexed (at the simplest level) towards the polyhedra and subsequent side of that polyhedra to which it abuts (if any, and not a complete boundary, i.e. a wall), but while normally it would be a 1:1 matching for all phenomena (or with outright exceptions, such as "invisible forcewall" preventing physical movement but allowing vision, and "energy barrier" allowing everything through but certain classes of weapon discharge, "glass" being like the invisible forcewall but able to be "smashed" and revoked by any physical weapon discharge of sufficient power) there were possibilities of making physical transit and optical transit progress into alternate 'target' polyhedra (with equivalent 'receptive' surface), which I suppose one could liken to a "stargate, without the rippling pool effect" (though you could have given it a rippling pool effect as well, remember how old this idea was... I can't remember when Stargate first popped into my consciousness). Alongside other interesting possibilities[1], this meant that the environment could involve 'overlaid' polyhedra where the physical and optical aspects could pass through alternate 'overlaid' dimensions in the same logical space.
So...
if we could not establish every zone to be 'one-size fits all' and be able to pack all necessary border-to-border passagability information into each, it would not be too difficult to have transit from one zone (say an internal zone, entirely constrained by the bedrock, and thus pretty much the same to any creature that hadn't a tunelling capability to fall back on) guided by the zone-boundary definition to split so that surface travellers make use of a 'surface friendly' target zone, one of many overlaying the landscape that are interupted by trees and channels and other impassables, while aerial creatures are free to fly into the 'atmospheric'-styled zone, which may still have trees as obstacles at the surface (either zone limiters in Z-spanning convex polyhedra, or singular features to avoid within that) but treats channels as vertical borders into 'deep ditch' zones with aerial access possibilities, or can be ignored and passed over. The 'logical' positions of ground-dwellers in the surface-zoning would be known within the aerial-zoning hierarchy through passing the absolute cartesian coordinates between the two, so allowing appropriate pathing and 'hunting' of ground dwellers by aerial ones (despite inhabitting a different 'zone-space') and a ground-based archer would have no problem targetting a flyer. If the surface-pather was amphibious and passed into an aquatic-styled zone to swim below the surface, this would put them beyond a non-transitable boundary as far as any particicular aerial agent was concerned, if it was hunting and not an aquatic-capable creature (e.g. gannet) able to undertake that transit.
[1] Scaled travel: i.e. transit between polyhedra surfaces of differing areas, essentially altered the avatar's relative size in the environment if he looped back to origin via a different route ('Distorted' travel, also, where the avatar changes relative width and height).
Mono-directionality in some/all of the physical/optical/sonic/etc propogations.
"Movable holes" in the environment, that could be slide around one one
or both sides.
Simple implementation of mirrors (back then Duke Nukem 3D hadn't popped up, so I'd not seen it done) by linking the optical 'outward' transit to the same facet of the polygon
Rooms with a rotational symmetry of 0.5, where you have to walk around the central pillar 'twice' to get back to your original position.
Some of the above was inspired by "Toonyverse" physics, I'm sure you can imagine.[/1]