Any reason I should not go with your everyday rebuilt master cylinder to replace the one going bad on my truck? Thinking there should not be any big difference between the one from Autozone and one from the dealer...

You can go with autozone cheapie but remember you get what you pay for. Then again my 82 has a cheapie M/C on it, about 4 years ago and it's still fine

For a few bucks more, you probably would do better at NAPA.