I’m pretty sure they are considering the air flows at different altitudes.
I do remember an article saying that the National Weather Service in Omaha, Nebraska was sending extra weather balloons down there for this purpose.
The question I’ve got, though, is whether the models are truly ready to take that extra information into account. Because this degree of scrutiny of atmospheric conditions is not common.
Maybe if Irma does something drastically different than the mainstream projections, the experience with her will be factored into new models.