- Why do the reanimating effect extend underground, if the caverns are nog affected by allignment?
I suspect because that'd be too easy to exploit. Just make sure that all (re)killing takes place properly underground, like any decent dwarven dug-out[1] fortress is already skewed towards, and you'd just have "odd guests" (and the perfectly normal issues of immigrants/traders being in trouble if they're not brought inside and turtled ASAP), not an undead cascade with creepy crawling hands/etc like it might be intended.
Maybe I'd have allowed for a (hidden-variable) contact-trace version of reanimation. A chance that anything (initial expedition, migrants, visitors, traders, wildlife, possibly items/liquids) that passed through a reanimating zone carry with them an environmental chance to reanimate which 'decays' (half-life-like) but also propogates (again, a slight chance only), such that a death of anything with the lingering curse still upon them can reanimate. Makes more sense than a hard-bordered "from Circus to sky" column of inevitability, introduces a chance to take precautions but still an off-chance of a Summoning Dark sort of thing possibly biding its time until a suitable opportunity to arise.
Or a proximity thing. A (say) 10-or-more-tile (x,y,z-wise) passing-on-zone from any surface-effected undead that ignores absolutely all barriers for the purposes of 'reinfecting of dead things with undeadness', which adds at least a trivial level of confounding towards a player's inevitable isolationist tactics.
Both the above would also make the boundary fuzzy, but (practically) make it not a world-spreading 'virus' if allowed to do its stuff even over worldgen/beyond-embark world simulations of consequential effects.
...but, in leiu of that, making it a subterrainean penalty at the same degree as it is a surface one adds the known jeopardy without rendering it potentially inconsequential. (If that's how it works, for any given playing style.)
[1] Constructed surface-forts/aboveground buildings (roof above but still "outside") might still be dangerous, but 'dealing with' undeadnicity merely by balancing against dark-adaption and its disadvantages seems a bit lop-sided a way to easily mitigate what is supposed to be a challenge.