Perhaps in my playing around with the L system I managed to muddle things up, but it appears to me that the bit of code inserting the race-specific "farmhouses" on worked farms overwrites the code for the farms themselves to change according to the owning civ's religion.
Assuming that it's even possible, I can see how tedious it would be to create entries for every civ's unique farmhouse (governed by "Artstyle") on every religion's unique farm .nif (governed by "Era"). 21 Civs x 7 Eras x 4 entries per leaf x however many leafs relate to farms. But suppose I wanted to set Era=Veil for all Sheaim cities and Era=Empyrean for all Malakim ones. Before I dive in blindly and spend hours trying to accomplish this, I figure it'd be worth asking if anyone knew the correct way of going about this.
Edit: Okay, so by replacing BLeafs 2x1 through 4x2 with the original FFH's data, farms will appear in any religion's color with any civ's farmhouse, depending on the Era. The unique Ljo farm-trees are lost, but it otherwise seems to work normally. Now I'm a bit curious as to when a civ following the RoK religion will be in the Runes Era and when it will be in the Classical Era.