I always preferred the idea that the whole thing was a dream because it starts in media res and jump cuts a lot with tales of vaguely explained agents and conspiracies.
But seriously, Nolan built the film from the ground up to make emotional sense and to resonate with the emotional themes as he says
The important thing is that Cobb?s not looking at the top. He doesn?t care.
and
For the ambiguity at the end to work, you need to see that Cobb?s world and the dream world are very similar. And you need to doubt Cobb
So although it probably is a plot hole, it's not one that matters. You could say that since the inceoptioners are able to mildly interact with the world and chance aspects of it, and that Cobb fiddled with the creation of the dream even though he said he wouldn't, and that he's once of the best creators there is, that Mal isn't actually a projection, but gives all the presentation of one because that's what Cobb has created her to be like. His subsconscious interferes with the creative process and always remind him of his wife and creates here as 'projection' in the dream, in the same way dreamers can create guns or clothes.
Her sophistication is a testament to the flexibility and exceptional imaginative power of Cobbs mind.
Thats not the actual answer and there doesn't need to be an answer, but I'd like to see if it's got holes or not. We know dreamers can create things in the world, so there shouldn't be a reason why they can't create things that look like projections, as long as they're good enough