the recipe editor doesn't care how long you boil in terms of gravity. it just cares about boil off amount to calculate OG.
changing the boil time in the editor only affects IBUs, as it should. 5 min or 50 min boil result in different IBUs.
Make sure you know you're boil off rate on your setup. In 60 min I typically boil off 3 quarts, so I know to put my boil size as 3 gallon and my ending kettle as 2.25 gallon. my ending fermenter value is different because I typically pitch a 1 liter starter on it, raising my fermenter target to ~2.5 gallon, and I compensate it with a late addition value of DME in the recipe. The editor is reading my recipe as going 3 -> 2.25. And speaking strictly in terms of gravity, it doesn't care how fast you boil off all that amount, it only cares where you're starting your boil and where you're ending your boil, and not when you're starting and ending.
now obviously boiling for 1 min and 120 min will actually affect your OG, but you still need to know your boil off rate and adjust.
If I set my boil size to 3 gallons and I set the boil time to 1 min, I would need to set my ending kettle to 3 gallons, because that's no time to boil anything off.
If I set my boil size to 3 gallons and I set the boil time to 120 min, I would need to set my ending kettle to 1.5 gallons, because I typically boil .75 gallons per hour.