This is something I have 'struggled' with for quite some time (I put 'struggled' in quotes because I really haven't given it
too much thought besides "oh when I mod Naga I should make them use Pylons like Protoss" and that's it
). I feel like it shouldn't be too hard, but then again...
#1, are you currently using "Blight" in your project? If not, that's half the battle; just make a "pylon" unit that makes Blight in a circle, and it'll only allow buildings built there.
As for the "not working without Pylons"... Not sure. Perhaps a little hidden aura (Tornado Slow Aura is choice) & a trigger that catches whether a building tries to build/train/research/upgrade anything, stopping it if it doesn't have the buff?