The packaged weight is generally the other stuff you mentioned... guylines, stakes, stuff sacks, etc. There's no box or packing materials for tents such as the Hubba.
I usually find that adding ~4 ounces to the minimum weight gets me roughly to actual trail weight. That assumes light stakes & light guylines, but not using the stuff sacks (well, sometimes the stake one), & not carrying pole splints/etc.
The minimum weights of the two tents in question are 2 ounces different, w/the MSR listing as lighter... so yeah, it's probably going to weigh a hair under 3 pounds...