While it is true that imperfections in a marble block might slightly influence what gets carved, the carver will work AGAINST those imperfections if he is a traditional realist carver. If he is a modern artsy fartsy carver, then his inadequacies will translate into "truth to materials", and the imperfections will affect, or dominate, the end result, due to technical inability to work against them.
Direct carving was done from a modello, but not necessarily with a lot of measuring - no more than a competent artist would use during a life drawing session. Michelangelo had a well developed eye, and probably did not need to do a lot of mechanical measuring, that process would probably have been taking place in his head. There are a lot of unfinished Roman works around, so that a fairly accurate assessment of how a Roman went about carving a piece can be arrived at - and the Renaissance and modern methods of direct carving are pretty similar. Michelangelo might have used a pointing frame, and a full sized modello - certainly it was technically possible for a full sized modello to last for the necessary 3 or more years - and then again, he might not, indeed, I tend to think he didn't, after looking at unfinished works of his...... Certainly, most carvers throughout history working on large realistic works, have made pretty good quality modellos - the stone is too expensive to be able to afford the luxury of error on a grand scale. However, the modello is not always pointed from, except to "bone in" the main planes and tangents. The block used for David sat unused for many years, apparently, simply because it was so expensive. I also read somewhere that it had also been blocked out already for another sculptor's work, which was then not taken forwards. This stage would have taken place at the quarry.
Evan.