It's a tricky discussion in this thread because we're mixing together the questions of "Is this allowed (constitutional)?" and "Is this a good idea?" I believe that in both the Filburn case and in your hypothetical FOSS example, that yes, Congress has the power to regulate them.
But that doesn't mean it's a good idea. At some point, the elected representatives in Congress have to make a law to regulate the interstate commerce. In Filburn's case, a majority of the democratically-elected officials in Congress decided that price stabilization of crops was important enough to restrict growing "private stashes" that weren't going to be sold. If supporters of Filburn didn't agree with that, then they would have to elect new representatives to do overturn the law. (Which by the way, will probably finally happen sometime in the next decade.) But there is zero support in Congress for restricting FOSS, even when it competes with commercial software. The benefits of FOSS to all Americans are so obvious that it won't happen.
But that doesn't mean it's a good idea. At some point, the elected representatives in Congress have to make a law to regulate the interstate commerce. In Filburn's case, a majority of the democratically-elected officials in Congress decided that price stabilization of crops was important enough to restrict growing "private stashes" that weren't going to be sold. If supporters of Filburn didn't agree with that, then they would have to elect new representatives to do overturn the law. (Which by the way, will probably finally happen sometime in the next decade.) But there is zero support in Congress for restricting FOSS, even when it competes with commercial software. The benefits of FOSS to all Americans are so obvious that it won't happen.