For nearly all of my pens, I use Original Gorilla Glue, which is a polyurethane glue that foams. I have never had a tube push out from the foaming action.
To apply polyurethane glue, fill an old pill container with water to keep it handy. Use Q-tips to wet the inside of the holes in the blanks before inserting the pen tubes with the polyurethane glue on them. Put on a disposable glove and hold the tube with your gloved hand. "Spiral" the thick glue around the tube from the tip to near the end. Twist, pull, and push the tube until both the tube and blank are well-coated, then push the remainder of the tube in. Press in with your gloved thumb and sweep it sideways across the hole to wipe off the excess glue. Set the pen blanks down on their sides on a Rockler silicone mat or waxed paper. The glue will turn yellow, foam out, and harden. When the glue is cured, use a chisel to slice/scrape the foamed glue off the top of the blank. Use a pen mill insert by hand to twist/knock/cut out the glue plug from inside the tube. On VERY rare occasions, a rattail file is needed to scrape out excess glue from the tube. (I tried 99 Cent Store generic play-doh to plug the tubes, but it was messier. I bought dental wax for plugs, but have not tried it yet.)
I like how polyurethane glue expands to fill the gaps. I have seen tubes that are not perfectly centered in their holes, but very close, good enough that the pens turn out fine. Polyurethane glue takes 24 hours to cure. I have had pen failures associated with CA glue, but never with polyurethane.
I have used White Gorilla Glue, which is a polyurethane glue that dries white instead of yellow. It works equally well for pen tubes, but goes on more "runny" than original Gorilla Glue. It tends to flow and drip off the tube as you insert it, making more of a mess. Otherwise, it works as well as Original Gorilla Glue. It seems to harden and cure faster, but they still say 24 hours for a full cure.
I use cheap 5 minute epoxy from the double syringe for translucent plastics/acrylics. It works well, but is messy and expensive.
I use medium CA when I want to turn a pen immediately - usually for a demonstration or to make a pen "now." Spraying activator on each end of the blank seems to reduce chances of glue failure based on a friend's recommendation and personal experience, although I can't explain why.
I use Clear Gorilla Glue (silane, not polyurethane) on rare occasions for special needs.