With milspec tubes, the threads are rolled from the tube. This results in the thread diameter being slightly larger than that of the tube itself. With "commercial" tubes, the threads are cut into the tube- since both have the same thread diameter, you need to start with a slightly larger diameter tube.
In theory, milspec tubes (properly made) have a slightly stronger connection into the receiver due to the fit of the threads, but in practice, there's really no difference. If you're out there breaking commercial tubes, I kinda doubt that a milspec one (or the rest of your rifle, come to think of it) will last all that long with you anyway.
The only real concern is you need to remember which you have in case you decide to swap out stocks.