no need to glue them together before and some epoxy will get into the tube but it's just a matter of using a small screw driver to chisel it out once the top is cut off. just make sure the two pieces of tube are cut clean and relatively straight and push them together as you clamp down on the filler piece that covers them.
you do get a slight seam that you have to sand down to make the transition smooth but a little epoxy coat hides both the seam and the portion you sand. as for both pieces lining up straight, the tubes will be forces to the bottom of the track you cut with the 7/16'' bull nose bit even though the tube is a bit thinner the filler piece will keep them centered as long as it and the track is cut straight.
hope that helps.