I think its wrong to call this a "loophole." That term implies that someone is doing something negative, when, in reality, they are just taking advantage of what the law allows. I am convinced that if lawmakers do not like "lopholes," they can close them (something they often do). If the "loophole" remains unclosed, then it is your legal right to use it and, frankly, you'd be stupid not to.

If the feds are not in control of the lines leading up to the machines than the airlines are free to arrange them however they like. I doubt the feds will move to close this "lophole" as it is unlikely they have jurisdiction. If someone brings a lawsuit, so be it. They will be very hard pressed to establish that lines which are under a private entity's control are violative of the equal protection clause of the Constitution (this being the likely legal avenue such a plaintiff would take). There is some support for having the equal protection clause apply to private entities that are "significantly entwined" with a government entity, but the fact that one the line can be separated from the screening machines makes this unlikely to succeed.