It's probably not possible, but if there was some kind of scale parameter that could shrink objects within the map, I'm sure it would break the level design and look weird, with objects floating or anchored to points that don't make physical sense. The XBox limitations required them to make some hard trades on map size, level of detail, and the scale of places. Without an editor available, it would take a total re-make to expand the levels. However, it might be possible to make Alex shorter, if there is a parameter somewhere that specifies the camera height above whatever surface you're standing on. That wouldn't do much to the apparent scale of places like Liberty Island, but it might make doors and ceilings feel taller.
FWIW, I've never noticed issues with door height or ceiling height, but the lack of believable scale stands out in a lot of places, especially the hubs. And some areas have been pared down to the bare essentials needed to support the story, with the hope that players can imagine the rest. Sometimes it works for me, like the medina apartment building which is just big enough. Sometimes it doesn't, like lower Seattle.
I've played this game 4 or 5 times. I always enjoy it right up until Liberty Island. But the problems with Liberty Island go way beyond it's physical size.