Youre right, amount of water in the boil itself will affect hop utilization. Partial boil brewers will have to ramp up the bittering additions in particular when following a full boil recipe. IF, that is, you're trying to get as close to the original as possible. That's something beer software does really well.
Different beer software may also yield different results from one another. To make things even more difficult they don't all account for time of extract addition which also affects utilization. Of course, they also do not account for each minute detail of the brewer's individual process, a huge variable.
Fortunately we can ask the recipe creator questions on this forum if a detail isn't included, like boil size, addition time, fermentation temp and schedule, etc. Seems to me thats the best way to get as close as possible to the original.