1. If you use polyurethane glue (Gorilla glue) it will show.
2. if you are turning a very translucent acrylic, and your epoxy isn't perfectly smoothly applied, you can see the swirls and voids in the epoxy through the blank.
I guess it just boils down to how important it is to you how the pen looks.
3. If you scuff your blanks to make the glue stick better, the paint you apply to the tube can cover the scuffs so the glue doesn't adhere tightly.
4. Painting the inside of the blank is just as easy as painting the tube.