I am a little confused by your comment that the measured OG was 1.046 and yet at the end you said you ended up with an OG of 1.044. Was the 'meas OG' cited in the beginning one that was already in the recipe when you opened it? If the number was already in the recipe as you downloaded it, then you can pretty much ignore the number with regard to the basic recipe as it may have been someone else's results or just default numbers no one bothered to reset. Without knowing which, ignore all 'meas' inputs as they are for the brewer to enter in their own measured values to compare to the estimated values from the program.
You are correct in thinking that the Brew house efficiency is most likely different from your process. This can come in in various places: (1) lower mash efficiency extracting fewer sugars than the recipe called for or (2) greater process losses in your system leading to greater demand for water (lowering the gravity).
Next, did you 'scale' the recipe to your personalized equipment profile or did you brew the recipe as it was downloaded? If you did not use your own equipment profile that matched your equipment and process then that might explain quite a bit of the difference. Your process losses are probably not the same as the original recipe builder. Your boil off rate may be much different. Your crush and sugar extraction from the mash may be different.
The nice thing about BeerSmith is how much of it can be customized to everyone's individual process and set up. It takes time and careful measurements of volumes and gravity through out your process to get teh correct information and then updating the equipment profile to get the software to match what your process output will achieve.