Hmmm... I can see your problem. The template was for a different probe. Ill update that. You would be better off with the inside hole larger than the probe so the internal wall doesnt act as a heatsink.
All the way in.
Its only the end of the probe that reads temperature but if everyone does the same then the readings will be similar.
Rust? I doubt it unless you planned on washing it in the dishwasher (joke! Dont do it!!!)
Using a larger drill bit in your fingers you should be able to twist it from the inside of the roaster to remove the burrs. If you were building these then you would use a "deburring tool" but an oversized (sharp) drill bit will work fine and wont remove the gal-coating like a file will.
phew... so many questions!