The pH rises when you increase the FC levels and for yellow/mustard algae you raise the FC A LOT. Lowering the pH first helps to lessen how far the pH rises and has the active chlorine level be higher as well. Ironically, having CYA in the water has the pH go even higher when you add chlorine compared to no CYA. For example, using a TA of 80, CYA of 70 ppm I get the following pH changes from raising the FC by the amounts indicated when using a hypochlorite source of chlorine.

Regular Shocking (from 5 ppm to 28 ppm FC so increasing 23 ppm FC)
pH goes from 7.5 to 8.7 (active chlorine 0.21)
pH goes from 7.2 to 8.2 (active chlorine 0.26)
pH goes from 7.1 to 7.9 (active chlorine 0.28)
pH goes from 7.0 to 7.5 (active chlorine 0.31)

Yellow/Mustard Shocking (from 5 ppm to 42 ppm FC so increasing 37 ppm FC)
pH goes from 7.5 to 9.0 (active chlorine 0.35)
pH goes from 7.2 to 8.7 (active chlorine 0.45)
pH goes from 7.1 to 8.5 (active chlorine 0.51)
pH goes from 7.0 to 8.3 (active chlorine 0.59)

The pH should drop back down at least part of the way as the FC drops, but during the shock treatment it would be better to not have the pH rise quite so much. Note that the main reason for the higher shock level is to get the level higher even in areas of poor circulation and to kill algae that has been established so has more protective layers (or is thicker). Technically, if you were able to access the algae wherever it hides and break it up, it wouldn't take so high a chlorine level.

If there were no CYA in the water, then adding 37 ppm FC with a starting pH of 7.5 would go to a pH of 8.0 instead of 9.0 shown above. Of course, with no CYA in the water one wouldn't need to shock so high (but chlorine would break down from sunlight quickly).

As for the advice about going to a regular shock level first, that's for pools that have a mixture of algae problems or where the overnight chlorine demand is high. The regular shock level gets rid of any green algae and chlorine demand without losing so much during the day from sunlight. After that stage, then shocking at the higher yellow/mustard alage level is done. In your case, you don't have other problems or chlorine demand so can start off right with the higher yellow/mustard algae shock level. This is the problem with trying to codify these sorts of things into rules -- there are too many unique situations to have a "one instruction for everyone" so posted instructions need to be seen more as guidelines while the forum experts can guide more specifically. Nevertheless, Ben's instructions are very thorough and work well in most cases; the TFP ones tend to be shorter and simpler and hence have more exceptions. Also, some things I've recommended (such as lowering the pH before shocking) don't get into such rules.