Everything deforms to some degree when you add stress, like tightening bolts. High performance engine blocks have a boring plate torqued onto them before boring the cylinders to simulate the deformation that happens to the block when you torque down the cylinder head. Most commonly its an iron block with aluminum cylinder head/s. Its somewhat counterintuitive to think the aluminum head can cause the block to deform but they absolutely do.
There are far too many different products from different manufacturers with varying tolerances to assume that everything is going to fit perfectly without twisting, warping, or some type of deformation when assembled and torqued, and therefore not need at least a little lapping.
In my particular case, I have a 110 Tactical with an EGW 20MOA rail, Arken Rings, and Bushnell Match Pro scope(rings & scope soon to be replaced). 4 different parts made in 4 different places with at least 4 different sets of tolerances.
There is a tolerance in the 110 receiver shape and where the holes are drilled, there is tolerance in the rail, both as it sits unmounted, and then any deformation that may occur when torquing it onto the action(because of its own tolerances and how those match up against the aforementioned tolerances in the action and screw holes). Then the rings have many tolerances in their construction.
Those tolerances can stack or negate each other, or most likely some combination of stacking and negating. But again to assume that everything lands at a sum of zero is foolish.
Any deformation at the rail is then multiplied by the rings because they are further from the mounting point(so .0005 at the rear point of mounting might be .0015 at the centerline of the rear ring bore, ASSUMING the ring is perfect. Then lets say the rail sits perfectly inline at the front mounting, and assuming the ring is perfect, you have .0015 misalignment between the centerline of the ring bores.
THEN the ring bores might not be perfectly square with the ring mounting, most likely adding even more misalignment OR possibly removing the misalignment but reducing the contact area.
Area 419's method(just an example, others may do the same thing) of boring and honing the bores as a pair HELPS this but you still have the possibility(I would say probability) of mounting those rings on a receiver/rail combo that is less than perfect.
On top of all of that, when lapping, we are assuming that the lapping bar is perfectly straight, perfectly round, exactly the correct diameter, with zero taper. But its far easier to make a perfectly straight, zero taper, 30mm single piece steel bar than perfect scope rings or rail.
Also to be fair, a lapping bar will wear over time(FAR less than the aluminum alloy of the rings, but its still wear) so at some point the lapping bar needs to be replaced.
ALSO alignment bars CAN be misleading. rings could be misaligned and the points still come together(as TaperPin below pointed out, as an extreme example, imagine mounting rings on each end of a banana, the points could come together but obviously the rings arent aligned). If they were doing things right, they would come with a simple piece of flat steel or aluminum(imagine the opposite of an axe blade angle gauge) with the combined angle of the points so that you can make sure the points come together inline and not at an angle.
NONE of this is questioning the quality of the parts used. EVERYTHING has manufacturing tolerances.