This is all addressed in the book. The point is NOT for conditioning; however that is a benefit. The point is to build a capacity that is so big/strong that you are able to easily handle (for example in the Krypteia program) 100lbs DB's for all DB lifts and not give it a second thought. We have 140lbs kids that can use 100 DB's for all squat sets and not blink an eye. But this is done OVERTIME and with an extreme amount of attention to EVERY detail of their training/form/programming.
The point is this: the timer is fine but should be an after thought. You should be in good enough shape that all sets can be done 100% perfect and 100% explosive and not have to worry about the time. That is why, as explained in the book, you keep a running timer as a guide in the beginning (not as a goal) and make sure the quality is there well before you try to reach a timed goal.
Quality is the MOST important. And again, conditioning is a happy after thought, not the point. Never was/is. Never should be in a strength training program.
Also, the Krypteia is NOT for everyone. This is also addressed in the book.
Lots of stuff addressed in the book.