If you started with 54L pre-boil, boiled for 60 minutes and ended with 51L, that's only about a 5% per hour reduction rate which is pretty low. While it varies widely depending on kettle dimensions and a few other variables, an average boil-off rate of around 14% is commonly accepted at the home-brew level, which also happens to be about what it appears BeerSmith was telling you.
Doesn't matter if you left the lid on at the beginning, many of us do this to conserve a little heat energy at the start. It's the intensity of the boil that matters. Sounds like your boil was lacking in intensity. Easy fix - boil harder next time, but be sure to watch out for boil-overs if your kettle is fairly full.
Something else I see - you're topping-up in the kettle. If you're doing this to hit pre-boil volume, that's fine if you're already above your estimated pre-boil gravity because you're diluting the wort down to what you expected by adding straight water.
If you came up short on volume AND gravity, seeing as the boil accomplishes a reduction in volume resulting in a concentration of sugars, you'd want to pull more sugars from the grain. Assuming a batch sparge, You can toss some more sparge water in the tun, stir, wait a few minutes, recirculate until clear, and run that off to the kettle until you hit your volume and pre-boil gravity targets. If you fly-sparge, just keep running until you've hit your targets (this assumes you have enough water in your HLT). Even if you end up with a little more liquid in the kettle than anticipated, just boil a little longer, no biggie.
As long as you're still pulling sugars from the grains, you can continue to sparge, just watch the pH and SG, don't go above pH 5.8 or below about SG 1.010. You may need to make more sparge water than BS tells you - I make around 5 gallons of sparge water every time (I brew 5 gallon batches) and even if I don't use all of it (I rarely do), it's good to have on hand for just such an emergency.
Your gravity tanked because you diluted 43L of an already short-on-gravity wort with 11L of straight water, and only boiled-off 3 of those liters. If that top-up water had contained sugars from the grain, you would've been further concentrating that liquid and likely would've come much closer to your gravity target. It takes practice getting used to how your system works - keep plugging away and take lots of notes - you'll get there.