Became alarmed to this topic when helping a friend to tear apart an engine that developed a through-bolt leak immediately after a full rebuild. We found one of the standard blue O-rings squeezed to the outside between the flat side of the washer and the block.
In general the geometry/chamfer of washer and block should keep the O-ring centered when you fasten the nut and press the O-ring into the remaining cavity, while the resulting elastic deformation of the O-ring will seal against the bolt surface. Attached two pictures where you see how the O-ring moves inwards if you clamp the washer down and the chamfer comes into play. (used the standard blue O-rings just for this exercise). When you push down on the washer you can almost feel how the O-ring “moves into position”. With the bolt in place of course there is less room for the O-ring to move and if something goes wrong it might bow out into the wrong direction ending caught-up between washer and block.
Several factors might play a role:
No or not enough lubricant on O-ring.
No or not enough chamfer on through-holes.
Washer turning while fastening nut.
O-ring material too stiff or temperature too cold.
Wrong O-ring dimensions.
Excessive play between washer and bolt allowing washer to be off-angle.
Fastening too fast e.g. by using an impact wrench.
So I guess if you follow the typical recommendations (correct O-rings, lubricants, chamfer, no spinning washers..) the risk to mangle up an O-ring are actually quite low. Just take care and no rush for each of the 24 bolts.