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The main difference between commercial and mil-spec stocks is a slight difference in the buffer tube diameter. I believe the commercial tube is 1.17" and the mil-spec tube is 1.14". However, the thread size is essentially the same on both so you can screw either size tube into any mil-spec lower receiver. The stock body inside diameters also vary. The inside diameter of a mil-spec stock body is just over 1.14" so obviously it will not fit a 1.17" buffer tube. A commercial stock body has an I.D. of just over 1.17 so it will fit on a 1.14" mil-spec tube but will rattle a lot. Just make sure that the complete assembly (stock body & buffer tube) are either both mil-spec or both commercial. The internal components (buffer & buffer spring) are interchangeable for either buffer tube size.
You can use any tube you want as long as the same depth/length of the JR-tube is maintained. If the travel is shortened, you will run into more feeding/cycling problems. If the travel is increased you will break the charging handle as it slams into the upper receiver.