The dark arts of revenue management at work: that department knows the profile of passengers on that sector (as in, how much they like to spend, how soon they buy them in advance etc.) as well as projected standby/non-rev fares as well as cargo payload. What looks like totally full in Y may only be 90% paying customers, or it may have been overbooked, but EK know that route doesn't sell last minute J or F fares, but does sell last minute Y fares, but only at x price, so opens even inventory at >100% capacity in Y and pushes people up to J (or F as required).

Last minute cheapest available Y fares strikes me more as "there is little chance we can get any extra expensive fares so we might as well open an offer up and see if anyone bites". No revenue manager worth his/her salt wants to allow staff tickets on board It is quite not uncommon on EK for staff to get offloaded even when there are seats available because some revenue paying cargo business has come their way at the last minute (or for instance, lots and lots of pax baggage and juicy excess charges that come with it).