Regardless of what you intend to decorate the inside of your tubes with, I think the solution is to apply the adhesive on the inside first and then decorate.
I was looking at a way to get paint brush bristles angled at 90 degrees either via a kludge, like an elastic, or a commercial product but I had issues searching for "90 degree brush head". What little I did find was either too large or unrealistic for this application. That's when it hit me! There is a simpler solution likely already in your possession or at least cheap to acquire for this.
A toothbrush already has the 90 degree angle that would make for easy adhesive application on the inside of a tube. You basic white glue would be fine here for this. Even though it is non toxic I am sure you would prefer to get a dedicated toothbrush as supposed to dual purposing your daily one.
Once you get a decent amount of glue inside I would roll up the paper, that you plan on placing inside, smaller than that of the toilet paper roll itself. Gently put it in the tube and once it is inside all the way you should be able to release it. It will open most of the way and a little massaging will help get it in place the rest of the way. This should help keep glue from getting on the paper where it will be seen.
Using paper that is longer than your tube would be useful as you can adjust it from both ends without having to put your hand in too far. Excess paper can easily be removed with scissors or knives after.
If you were to use something other than paper, like glitter for instance, it would just be a matter of sprinkling it inside the tube and letting it stick.