The first thing to remember is that if you are off by 1/4" or 1/2" from the perfect measurement, it's not the difference between working and not working. It might be slightly less efficient...or not. There are so many variables in antenna performance that even building exactly to spec may not mean you get the same results. You may get better, or worse.
Next, the article specifies drilling the holes 1/4" or 1/2" from the end of the PVC. PVC is a little brittle, so I would lean towards the 1/2" mark. Next you don't need the measurement of the director to the driven element. Place the director at the end of the boom (minus 1/2"). The driven element is measured off the reflector in this design.
Lastly, the article was also talking about 3/4" pipe, so everything should work out fine. Last thing to know is that PVC will break down over time in UV light, not a big deal, it would take a few years, but it will get chalky and then (more) brittle. Options are to paint it or to not worry about it. If you are still in the hobby by that time, you will likely have replaced the antenna anyway.
Also, you can use a boom that's longer than specified to give you a little more meat to drill on. If it were 2" longer on both ends, it would not affect the performance of the antenna at all. Though you would have to measure the location of the director as if the boom half were still 18" as shown.