Usually, the reason why there are multiple stages for torquing is due to there being more than one fastener involved. For instance, there are several head bolts which hold a head in place. If you were to torque each of these in one pass, the torque would not be equally applied throughout the head and would cause it to warp upon first startup. A single pass torque is usually for things which only require one fastener to hold things tight, such as a wheel bearing nut. Since everything is handled by the single large nut, you only need to do it in one pass.
As for Torque to Yield (T2Y) fasteners you are suggesting, which are usually the type which fasteners used by many manufacturers today, they are single use fasteners and must be replaced. There is a subtle difference as per what Solar Mike has stated and their actual purpose. All bolts stretch during the torquing process. It is this stretch which keeps what is being held in place securely.
The difference between T2Y bolts and normal bolts is that the T2Y bolts plastically deform. As they are torqued, they stretch beyond their original length, yet hold the part securely. Once pulled off, they are deformed and should not be used again (though you'll find some who swear by them and will use them again ... not something I'd call smart, but each to their own). This is because they are already stretched and will not stretch the same again.
Multi-pass fasteners can be either T2Y or normal bolts. Usually, when you see a bolt which is staged with a torque and either one angle stage (in a two-stage torque sequence) or two angle stages (in a three stage torque sequence), these are T2Y bolts. Those which have multi-pass torque stages but no angle sequence, are normally reusable.
