Data doesn't actually live on a manifold. It's an approximation used for thinking about data. Near total majority, if not 100%, of the useful things done in deep learning have come from not thinking about topology in any way. Deep learning is not applied anything, it's an empirical field advanced mostly by trial and error and, sure, a few intuitions coming from theory (that was not topology).
I cannot understand this prideful resentment of theory common among self-described practitioners. Even if existing theory is inadequate, would an operating theory not be beneficial? Or is the mystique combined with guess&check drudgery job security?
There is an enormous amount of theory used in the various parts of building models, there just isn't an overarching theory at the very most convenient level of abstraction.
It almost has to be this way. If there was some neat theory, people would use it and build even more complex things on top of it in an experimental way and then so on.