There are many scenarios where separate PNR's are the way to go:
1. Simple return flight on reward points. Secure the outbound reward seat as soon as it's available. Book the return leg later when it becomes available. If you wait until you can get both on the same booking, you run the risk that leg 1 has been sold.
2. Staging flight to Asia to pick up a cheap premium fare onward to europe. This is quite a good option as long as you lay up for 1 night each way so you have some "fat" in your plan. This also works for classic rewards when you can find seats from asia to europe but the sector to AU is unavailable (which is quite common).
3. Travelling routings that aren't "allowed" on one PNR. Eg: As described in linked post, I wanted to fly from AU to Alaska one stop. Solution was a "nested" ticket via Hawaii.
This trip had us taking off in Sydney in warm autumn sunshine, and touching down in this:
www.australianfrequentflyer.com.au
Two PNR's allows SYD - HNL -ANC
One PNR means you have to do SYD - LAX - SEA - ANC. Yuck!