What's most irksome and irresponsible of SD is that they have claimed that their game is mod-friendly when in reality it is not.
It's friendly enough when it comes to the *real* simple stuff, such as adding an item. But yeah, it gets a bit frustrating once you get into more complicated stuff.... and as per your OP the inconsistencies are one of the major frustrations. Not being able to change anything to do with tech trees from the mod folder is a good example.
It's a shame such awesome tools like the particle forge get wasted.
Agreed particle forge is great. I found it's probably the least frustrating of the supplied tools.