I would not be surprised if FFG doesn't care about head swaps on Rebels, but the Empire is a different story. Besides armour colours, what is the difference between the armour of a Stormtrooper and a Death Trooper? The helmet. Many people love the new Death Troopers and lots of people on these forums have posted a desire to paint their Stormtroopers black, which by itself might make identification difficult at a glance once Death Troopers are released. If they also went so far as to replace the head with a 3rd party "Malice trooper", then the only difference is the equipment, and now the unit has become more difficult to identify.
I am aware Death Troopers have not even been hinted at yet, but I HIGHLY doubt that FFG won't release them at some point before delving into some of the more esoteric trooper unit options for the Empire. (Perhaps a wave of Krennic and Death Troopers with Saw and his Partisans but I digress).
40k minis are also more readily available, whereas FFG is known for having minor supply chain issues. It's a little harder for me to risk cutting up a mini if I don't know I'll be able to easily source a replacement by the time I need it for my next game.