Sotomayor seems to be angling to be the new John Paul Stevens in that she seems to be the dissenter most willing to use, to put it politely, "creative" reasoning to get to the conclusion she wants. Whether or not a bump-stock or any other accessory turns a semi-automatic firearm into "functionally" a machine gun is irrelevant. Thomas and the rest of the majority made the correct decision for two reasons.
1. A machine gun is, legally, very specifically defined and bump stocks do not meet that specific definition ergo, bump stocks are not illegal.
2. Because a machine gun is so specifically legally defined and ATF does not have the power to make or change law (only congress can do that) then ATF does not have the authority without an act of congress to redefine what is or is not a machine gun including bump stocks.
It seems to me that Sotomayor is attempting to argue that while bump stocks may not violate the letter of the law, they violate its spirit or intent. While this is probably true, the letter of the law is all that really matters as there have been plenty of people convicted and sent to prison who, while complying with the spirit or intent of the law, violated its letter, often unintentionally. A situation where one can comply with the letter of a law, rule, or regulation but completely contradict is intention or vice-versa is a classic case of unintended consequences and the fault for such a situation rests not with the people who take advantage of it or are victimized by it, but squarely on the shoulders of the people who made such poorly thought out laws, rules, or regulations.
Actually, Sotomayor's argument brings up another point that I doubt she meant to, but I think is worthy of exploration. If the NFA's prohibitions on machine guns (bump stocks, binary triggers, forced-reset triggers), and short-barrel rifles and shotguns (pistol braces) are so easily side-stepped, then of what use is the NFA? If we suppose for a moment that Sotomayor is correct in that bump-stocks turn semi-automatic weapons "functionally if not legally" into machine guns or that pistol braces turn handguns "functionally if not legally" into short-barreled rifles, then why do we not have motorized bandits running amok and blood running in the streets? What I think Sotomayor and others like her haven't thought about is that her "walks like a duck and quacks like a duck" argument cuts both ways. If you can so easily have something that creates a "functional equivalent" to an NFA item yet we don't seem to have the problems that the NFA is supposed to prevent, they why are NFA items worth regulating to begin with?