I get to jump in on this one (note while I was making a wonderful missive Brain jumped in line and beat me to it, his version is better! - forgot to mention the primers but cases also play a part)
I don't mind the question, good one though you can Google it you don't get the active discussion. Enough views (opinions) and you an form your own idea of what valid.
Probably the first one (my opinion) is how conservative the maker of the manual is. Falls into two groups, those who make bullets and those who make powder. Mine are bullet maker manuals, no powder though I do ref the power companies on line.
Just an aside my go to manuals are Sierra and Hornady as they provide a wide range of bullets as well as a wider range of powder listings than others. Even if you don't use their bullets they almost certainly have a weight and close profile of everyone else's.
Both list Rifle, twist and barrel length tested with.
The other has to do with what rifle (or test setup) they do their testing in. That also changes things a lot.
In older manuals the load levels were hotter, but also keep in mind powder has changed some as well so stay with current manuals.
I look at all my sources and select usually a mid range load to start with, but that's me, I just bench shoot and am not after hot loads.
You should be safe is you stay conservatively inside the limits of the two widest listings
Pressure signs are an elusive thing and the best check is a chronograph to see if you get a sudden increase in velocity if you are in the upper end.
All guns are different so the results are going to be different.
Powder lots vary as well. You would need to know the person who does the test protocol in each organization to really understand what drives them, you can only get a general outsider idea of the variances involved (and probably people bias in each organization as well not to mention legal)