Thanks for the advice Marco...
The reason i plumped for 3:36 per km (bang on my target pace to aim for a full 5km) was that in my recent block of training, my last rep session had been 4 x 1.25km at 3:45 pace, on a twisty-turny and by no means flat section of my local parkrun course.... then when i did my 5km time-trial i was able to replicate that pace over 5km on the flat and consistent running conditions of a track (i actually averaged 3:44/km on the time-trial).... so it's just based on my personal experience rather than any accepted science or theory.
Although i completely understand your point that running faster over 1km, you'd expect some slowdown over 5km.
I'll certainly be doing shorter reps at a higher pace... i'd usually be looking for around 77-78secs for my 400mtr reps, which is more like 3:15/km