I think the "1 humanoid" thing is a little misleading. Lily counts as a creature in the GECK, just like Rex and ED-E, yet she appears to fall under the "humanoid" category for the purposes of the companion limit.
Still, I guess this is why they didn't say "1 NPC, 1 creature".
Don't ghouls also count as creatures, like Super Mutants? I kind of wish that Lily and Raul didn't count towards the one humanoid limit, I was disappointed when I heard about it, hoping I could have both Veronica and Raul at the same time, and that they'd have some interesting interaction with each other (I really miss games where your party of companions actually bantered with each other).