Not sure which engine does the right thing so:
In many cases "lightfloor" UDMF property is applied differently to floor and things when said floor and things are below a 3d floor:
zdoom-2.9pre-1528:
gzdoom-g2.3pre-306:
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As the name says, 'lightfloor' should ONLY light the floor, and never any actor in the sector or anything else. It seems like the software renderer's lighting code does not pick the light from the 3D lists but from the floor in some situations.