Don’t perform the Zone 2 section of the RAe6 in Zone 3. The RAe series was designed for 70.3 and IM training, and only appears once in the Oly plans to get in some aerobic interval work. Those instructions are default instructions for that workout which do not apply to the Oly plan, and I’ll edit them now in the Oly plans.
Perform the RAe6 Zone 2 intervals at no higher than Zone 2 in your Oly plan.
Regarding the Zone 1 to 2 segments, you should still consider upper Zone 2 for these intervals, which at 4×15 minutes is not terribly hard, but not too easy to do consistently. Those Zone 1 recoveries ensure you can maintain a stable set of 4×15 intervals.