The only reason this would matter is if one student is Pell eligible, and the other isn’t. But if $1000 is 10% difference…that doesn’t sound like it would be the case.
In terms of need based aid, yes, the Profile schools will use the Profile information.
Have you run net price calculators for these two students? Really, that’s more important for the one who is a freshman (or both if both will be freshmen).
Just remember that at Profile schools, your family contribution will be at least 60% of what it would be for one student…at least. It’s not 50/50, it’s 60/60.