In thoery (and if the brakes are assembled correctly), the caliper will be parallel with the rotor when the pads are half-worn. When the pads are new, the caliper is closer to the rotor, which creates a slight angle from parallel. Likewise, when the pads are fully worn, the caliper is farther away from the rotor, also creating a slight angle from parallel, but opposite from when the pads are new. So, as the pads wear from new to worn, the caliper moves farther away from the rotor, and from being at a slight angle in one direction to being at a slight angle in the opposite direction, passing through parallel in the middle of the wear life of the pads.
The inboard pad (closest to the wheel) has a raised center on the backside, which creates a high-center as it sits in the holder, and this allows that pad to wobble as necessary to maintain parallel alignment with the rotor throughout the life of the pad, regardless of the slight angle that the caliper has with the rotor. It is important that the cotter pin that retains the pad in its holder is not too tight, as this can restrict the wobble that is necessary for correct pad-to-rotor alignment.
The outboard pad (at the caliper) typically wants to remain parallel with the caliper piston, and so it begins to wear at the same slight angle as the caliper is to the rotor, until it develops full contact with the rotor. Then, this pad continues to wear at a slightly changing angle to maintain flat contact with the rotor as the opposite pads wears thinner and causes the caliper-to-rotor angle to change.
The effectiveness and the feel of the brakes are affected by the variances in pad-to-rotor contact, and so it is important to ensure that the pads are aligned correctly in the caliper and with the rotor. New pads will need some time and use to become fully bedded-in due to the wear angle that is typical for the outboard pad, and full stopping power won't be realized until after this occurs. Also, if the pads are close to being fully worn, the amount of brake fluid in the circuit is quite a bit more (since the piston is extended farther out), and this also affects the brake feel, so it is often considered good practice to replace the pads before they are fully worn.
If for instance, the pads were to always be replaced when they were 1/2 worn, then the caliper alignment would go from being at a certain angle when new, to being parallel at that 1/2 worn point. In this case, the caliper could be shimmed slightly away from the fork leg and towards the rotor to reduce the slight angle of the caliper when the pads are new, which reduces the bedding time of the outboard pad. This would also allow the caliper to become parallel with the rotor when the pads were about 1/4 worn, and create an angle in the opposite direction when the pads were 1/2 worn. In other words, deciding to retire pads earlier and shimming the caliper to reduce the off-parallel angle that is the nature of the stock caliper setup, can improve the feel of the brakes, especially when the pads are new and in the process of bedding in.
Attention to this type of detail is not going to transform the stock brakes, but it will ensure that they are able to provide all the performance and confidence inspiring feel that they should. Although the stock setup isn't modern, it isn't bad either, it just needs a bit more understanding and attention to perform at its best.
