The new modules only apply the quality effect on the level 2 modules.
And I also found out that in some modules the efficiency effect does not alter with quality.
Meaning the effect on a normal module is the same with a legendary module.

Can you list some specific examples (with numbers) for your statement?

This mod performs very simple summation up effects of component modules, and put a discounted sum in their resultant module.
This mod has absolutely no code to interfere what a legendary module being differed from epic or normal module. This part is purely handled by game engine.

Or are you using some mods that are messing up with quality tiers directly? That is the only possible way to cause that. (Where none of my mods have touched quality tiers yet.)

Sorry for the late reply.

The SE module 1 has no quality on energy consumption.
The SE module 2 has no energy consumption itself.
The EP module 1,2 and 3 have no energy consumption itself.
The SEP module 1,2 and 3 have no quality on energy consumption.
The SQ module 1 and 3 have no quality itself.
The SEQ module 1 has no quality on energy consumption and no quality itself.
The SEQ module 2 has no energy consumption itself.
The SEQ module 3 has no quality itself.
The EPQ module 1,2 and 3 have no energy consumption.
The SPQ module 1 and 3 have no quality itself.
The SPEQ module 1 and 3 have no quality on energy consumption an quality itself.
The SPEQ module 2 has no quality on energy consumption.