I can't speak for others and experts or other may disagree with what I do.
For me, it's easier to have the same body position in pretty much all cornering situations. That is to say that I always put my buttcrack right at the edge of the seat, my outside arm stretched with the outside elbow rested on the tank, the outside knee pressed against the tank, weighing on the outside peg, etc. With all that, the body position relative to the bike is pretty much locked in. The only difference is that I might tuck the inside knee in a little if I need a little more lean angle. Or I may move my body a little forward if I'm trail braking, and then slide my ass all the way back while cornering to give the rear tire a little more grip.
To further control the line in corner, I would either slightly roll off the throttle (to tighten the line) or twist it a little more (to widen the line).
In terms of margin of safety, in most cases, I'd stick with no more than 40 to 45 degrees of lean angle with my knee on the ground. By keeping the same body position all the time, I know that when the puck lands, that's right about 40 to 45 degrees without the need to guess where I'm. And I can then focus on the track and the cornering line and throttle adjustments. Very rarely would I push it out beyond 45 degrees of lean angle, even though the tires can handle well in excess of 55 degrees.
And I might not get the knee down if the corner isn't tight enough. For example, in that big sweeper between turn 2 and turn 3 at Fontana, I would be doing 110 or 120 mph, hard accelerating with the bike in a no-more-than-20-degree lean angle. But the BP is still the same.
So there you have it. Again, that's how I do it; others may have different opinions on how to do it.