Another method of ensuring screws line up is to use the old-fashioned brace-type countersink. Drive the screw home, note the misalignment, remove the screw, countersink lightly, replace screw. Quite a bit of faff, and only for the very finest work.
The old countersinks used to be much more important in the 19th century than more recently. Standardisation of screw sizes didn't really happen until the early 20th century (I think), and fittings and brassware was often supplied with holes imperfectly sized and countersunk. It was therefore necessary for a craftsman to trim up his fittings with reamers and countersinks so that the screws fitted. The old brace bit sets always had a set of rimers (reamers) and countersinks of three types - flat (and quite hard) for iron fittings, rose for brass and snail for wood; often two sizes of each. There were three types of reamer, too - square for iron, half-round for brass and a sort of tapered gouge shape for wood. They all crop up quite regularly secondhand, and sell for peanuts because nobody needs them these days.
On brass screws, I think these didn't exist until about the middle of the 19th century. The reason being - as with tube for chisel handle ferrules - that drawn brass was not available, and cast brass was brittle and inconsistent (anybody who's fiddled with old saws having the split-nut fittings will be familiar with this); consequently, it was usual to use wrought iron screws to hold brass fittings in the first half of the 19th century. I think Derek Jones wrote something about this in F&C a few months ago, but I can't find it now. (Clock and instrument makers used cast brass for things like clock plates, but they hammered the blazes out of it to 'close the pores of the metal' and work-harden it - possible for screw blanks, but expensive if you've got thousands of them to make).
Edit to add - Found the Derek Jones reference - Furniture and Cabinetmaking issue 213, winter 2013, and follow-up editorial and letter in F&C 215 (Feb 2014) and 216 (March 2014).
