Ran into this issue on a server I'm on - since some vanilla dyes are annoying to produce, we tried substituting in Botania's floral powder, but train recipes call for the exact dye item, rather than asking for dyeRed, for example.
Could this be changed so recipes use the oredict instead?

Well. If I find where the heck we handle this in the code I can tell you if this is possible.

https://github.com/EternalBlueFlame/Traincraft-5/blob/1.7/src/main/java/train/common/recipes/AssemblyTableRecipes.java
Looks like in here.

Not really. This is only for other things. And we have no recipe for the dyes. They are handled very different without an recipe.

No this is exactly what I mean.
e.g. :
cm.addRecipe(1, null, new ItemStack(ItemIDs.ironBogie.item, 3), new ItemStack(ItemIDs.ironFrame.item, 2), new ItemStack(ingotIron.getItem(), 2), new ItemStack(ItemIDs.ironChimney.item, 1), new ItemStack(ItemIDs.ironCab.item, 1), new ItemStack(ItemIDs.ironBoiler.item, 2), new ItemStack(ItemIDs.ironFirebox.item, 1), new ItemStack(Items.water_bucket, 1), *****new ItemStack(Items.dye, 1, 2)*****, new ItemStack(ItemIDs.minecartLocoBR80_DB.item, 1), 1);
It directly calls for a dye item here, rather than an oredict

ah well you are referring to recipes in general. they will be redone for the 004 release.

added with e71fbb8