I played your mod a bit and came to the same conclusion - thing that mod really lacks is synthesis bracnches. And it is actually quite annoying. You can think about it like this: You have your mod that adds things to the game. Part of them are purely mod-related and supportive and part of them have some purpose by themselves. Purposeful things are the only things that justify the usage of your magic framework. For your mod situation is:
There are one-time rewards and it is equipment. It is currently not things like, you know, Philosopher Stone or sth like that - an ultimate thing that justifies everything. (BTW I highly recommend adding a Philosopher Stone or sth like that that justifies everything).
There are needed-in-small-quantities rewards and they are enchanced machines, modules and energy generators. They provide number-boosting effects but that's it.
And there is one infinite resource output, and it is wood.
So actually in a typical Factorio run building a thaumaturgical branch for your factory automatically becomes a lategame feature - it is not really justified while you're small because it gives you nothing but energy and speedup effects, when what you need is some qualitative changes like Robots and energy-only turrets.
(and it doesn't really help you to reach them)
BUT if you add some way to transform vanilla things one into another via thaumaturgucal means, thus altering optimal vanilla production chains, if you enable useful cycles and/or add some QUALITATIVE rewards (btw producing wood is a qualitative change because you cannot do it normally... although of limited usability), then you will see that hybrid thauma-whatever else factory starts to look more interesting - becomes more interesting to build - mod is much more attractive.
I can join your discussion on actual production chains if you want.