In my experience, an award upgrade offer requires a Y flex plus booking to be able to use the offer of lower miles instead of standard rate.

I have a couple of times used this kind of offer and usually it works out with no problem. Once I had to call Emirates to rectify right after booking as the upgrade page didn’t reflect the offer, only the standard upgrade rate. The agent on the phone should be able to se the upgrade offer associated with your booking and fix it, just stand firm on the offered rate.

What I am trying to say, if you see an award upgrade offer at the time of booking you should be able to get that. No guarantees however, if someone is able to snap the award offer ten seconds faster than you or something. But in general terms I would go for the offer.