OK, walk with me through this. You ended up with about 1.5 gallons extra after the mash. Your volume after mashing is recorded as 6.5 against a target of 9.2 gallons. Where is the extra 1.5 gallons?
Next your mash gravity reading is 1.010? Are you sure, because your pre-boil mash is then 1.046?
With the ending batch size being 7 gallons versus the target of 5.7, and the increase in OG from a target of 1.043 (without the honey) to 1.062 (is this with the honey?).
Assuming that your OG was taken with the honey (thus your comment about the addition of honey bringing you to 7 gal in the fermenter).
Gravity points check: (1.098 - 1) * 1000 *5.7 = 559
Gravity points check w/o honey added: (1.043 - 1) *1000 * 5.7 = 245
Actual readings: (1.062 - 1) * 1000 * 7 = 434, it would make sense that this is before you added the honey.
Of course, BeerSmith does not give you a place to put your actual volume before the honey was added, so that makes it difficult.
So you have some bad reading in the system somewhere. Let's throw out your post mash reading and put in your pre-boil measurement of 1.046 which would put your measured mash efficiency at 84.5% which is not unreasonable. Your measured brewhouse efficiency then becomes 41.2%, but I am figuring that your initial gravity reading does not include the honey. Am I correct so far?
So adding the gravity point the honey should give you, this gives you approximately 51 more gravity points and the additional volume would dilute this somewhat. Your note about adding an additional quart to top off the fermenter gives some clue.
It appears that since you ended up with a bit more sugar from the mash and less volume than anticipated, this ended up as a higher gravity going into the fermenter but with less volume. Because the program does not have a spot for recording the volume before honey addition, and it was not in your notes (which help by the way), I cannot comment too much further with out going into a lot of speculation.