Well, it does work seemless. If you are buying an KLM ticket for an DL operated flight you will be able to select a seat via KLM by beeing redirected to the DL website were you can select your seat. But KLM is telling DL that this pax has an seat in the "main cabin" and therefore you can only select seats within DL's Main cabin section. KLM will also tell DL's system that you are holding some kind of status that enables you to get access to the "preferred seats". So the system works seemless in this regard. It's Delta's fault that they handle their Y+ seats as a seperate cabin. As others pointed out you need to book an real "Premium Economy" ticket ( with AF for instance ) to get these seats on a DL operated flight. I know it sucks, happens to me all the time with lots of KLM tickets for TATL flights but it's excatly working as intended by Delta.
The good news: when buying an "light" fare via KLM or AF you will get a seat ( even the preferred section ) on DL flights right at booking as these are booking into N/V/X class and not into "E" as with Delta's basic economy fares.