Well, today I bit the bullet and decided to see just how deep the rabbit hole(s) went...
And the answer to the question of whether I could simply sand out the filled marks is: definitely not.
I started by carefully scraping away at the top of the filler, but soon realised it was more than just a surface fill. It turns out that all of the fill holes are pretty deep, with the factory filler varying from really rock hard to crusty on top and powdery underneath. Either way, it had to be removed. And the bonus is, I didn't spend hours sanding only to find I wouldn't be able to sand them out anyway. Bright side, bright side.
The fact that all of the holes are about the same depth also means it will probably be the same solution for all, rather than sanding out some, filling others, and/or worst case... plugging. At the moment, I still think that Timbermate is probably going to be my best option if I want to use Wudtone, so I'm going to do some tests over next day or two. Maybe try straight Timbermate, mixed with Wudtone, and mixed with sawdust options etc. However, if anyone has some suggestions, please let me know.
Here are the pics of the de-filled holes. The first set are all of the holes on the upper-bout/top, and the second set show the holes on the lower side, back and inside cutaway respectively.
http://pitbullguitars.com/wp-content...holes_1_md.jpg
http://pitbullguitars.com/wp-content...holes_2_md.jpg