Here is an update and reiteration of the issue that I'm encountering.
Structures generally larger than 10x10x10 (LxWxH) do not spawn in jungles or similar biomes that have their trees replaced by reccomplex's custom/user-made trees.
Altering the frequency options or weights of the structures have no noticeable effect upon their spawn rate.
Changing the generation type of a structure from 'Natural' to 'Vanilla Decoration' and selecting the option 'Tree', regardless of the transformers, drastically increases the structure spawn rate, in spite of structure sizes greater than 60x60x60. Unfortunately this increases the structures spawn rate so much that the weight need be turned down to <0.00.
From this one can conclude that the reccomplex 'Vanilla Decoration' option causes these structures spawning algorithms to run before the other types, thereby eliminating about 99% of all possible spawning locations for such structures.
Potential fix; ensure that the structures spawn algorithms run in sync so one does not invalidate the other.
So Ivorius, what do you make of this, is it fixable?