Considering that Vilcabamba is a real life city once inhabited by the Peruvian Inca, it makes me curious about its depiction in the Tomb Raider games. I have three ideas that could potentially explain the entire ordeal:
There's only one Vilcabamba in the TR universe, and it's the one depicted in TR1, strictly ruled by Qualopec.
Aside from their coincidental name, there are two separate Vilcabambas that don’t have much of a connection to each other. However, it's possible they could share a connection; for example, the real life version might've served as a diversion for the one in the Andes as a form of protection against Spanish colonisation of the Americas.
There appears to be two distinct Vilcabambas, but they're actually connected in ways that've been lost to time (e.g. a labyrinthine complex of subterranean tunnels) and are awaiting rediscovery.
I'm leaning more towards the third idea or an excellently crafted combination of the second and third ideas. However, the first one I presented could also be plausible because there's definitely some significant alternative history stuff within the lore of Tomb Raider and its sequels.
I went probably the easiest route myself and just made it the TR-equivalent of the real-life Incan Vilcabamba. Just like, say, Area 51 in real life must be pretty different from Area 51 in TR. So basically what you said at the end.
But if you want to have two separate Vilcabambas, you can totally have it be a coincidence, because there already *are* two in real life. Apart from the ruins in Peru, there's also a Vilcabamba in Ecuador, which is a still living city. And as far as I know (unless I'm mistaken), they're not connected in any way apart from having the same Incan name. (So I suppose it's like having several different cities names Springfield in the US.) So having, coincidentally, a third city with the same name sounds plausible.
The connection also sounds like a cool idea though! Either by physical connection, or perhaps just historical - perhaps they had to move for some reason, but named the new city Vilcabamba as well. Or they are just two halves of one city, even if it's not visible nowadays anymore. (The tunnels sound fun!). From your options, I think I like the third one the best too, even if it's not like that in my own headcanons :D
