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Am I completely blind, or does Epic 3rd edition (Epic 40k) not have any rules for infantry garrisoning buildings? I can find references to how they removed building destruction rules specifically because they made it too dangerous to occupy them, but I see nothing left about interacting with them in any way.

If you look at page 69 of the compendium (https://thehobby.zone/resources/Downloads/E40kCompendiumPDF.pdf), you'll find the terrain rules there.

Like in E:A after E40k, the terrain is an abstracted area rather than concrete pieces like individual buildings. An individual unit is in there or it isn't, depending on whether its base is within the terrain area. In E40k, the buildings raise the unit's armour value and make them harder to hit normally.

Ah thanks, and here's the HTML version: https://thehobby.zone/resources/e40k-compendium/Content/CoreRules/Terrain.htm

So if I wanted to play with LI-style buildings (which make it very convenient to position infantry on top), I think I would treat them as transparently passable to infantry as the rules suggest, and just put them on top when they are supposed to be "inside" the buildings. Looking at battle reports, it seems most Epic 40k games are played with hollow ruins, where this question does not crop up.

Pretty much, the vertical position rarely matters at this scale (besides obvious LoS questions like hillsides) so it's more of a "are you within the borders of terrain feature X" type question. Modern GW buildings work fine like this, too.

Can't remember if 3rd ed had a rule on how deep into terrain you can see, in 4th it'd be 10 cm and very large built-up areas would usually be represented by multiple patches with vehicle-navigable areas between them to avoid a situation where someone would hide objectives in large terrain pieces that could then only ever be claimed by infantry that would hide deep inside and remain mostly untouchable during the endgame.