Removing rotten wood -- Some use saws, other use other sharp instruments. For larger chunks, I like a very sharp timber framing chisel with a very long handle (a slick with out the offset bend at the socket-blade junction). If I do not find something that will look very attractive, it is waste and I keep removing material.
Grub tube remains = "frass" - the leaving that the larvae provide as it chews its way into/through the wood. I find I generally have to pick it out with dental picks if I want to remove it. It is a "design choice" as to how you want the outcome to look. The thin polymer solutions that are used for injection into woods are not very good at filling holes. That is a secondary process and again a matter of "design choice".
I turn woods with voids and often leave the voids as a "design choice". With pens, voids are less desirable and I have to chose how I want to proceed. Some cast resins, some use epoxy, some use CA glue. Each approach has advantages and disadvantages, especially if a longer time view is considered.
I have been moving towards making the stuff I am putting into cactus juice round before putting in the "juice". Two reasons -- 1. I want to see that I am getting something that I want to work with before investing the time and "juice". 2. I can reduce the amount of "juice" waste by not using it in the corners that I will turn away.
Design choices are yours ---- as are the techniques you use to achieve the desired outcomes. Every week I see new techniques popping up -- and older ones refined.