As it stands now the modules can be configured to allow higher or lower effects.
However, I would like to add/intensify a pollution effect to several modules to offset their usability.
Generally, I would like to be able to edit each type of module for the impact to all bonuses. This way lots of different setups can be chosen without having to write different mods for them.
I propose my personal imagined setup at the end of this post. I think it will balance the mod in such a way the production limit would no longer be an issue as the resulting facility would generate too much pollution to be worth it. At the same time it will keep its full usefulness and add an interesting difficulty.
Putting modules into every machine you have would become far less of a no-brainer, although the effects on critical machines would still be very much worth the while.
Notice as well that I give the pollution generating module bonuses (half speed& full production, but massive pollution and increased energy use).

I imagine this might be not all to difficult to code as it is just moving values from code that is already there into the settings screen.
In the mod settings screen it would then look like this:

Speed Module
speed: 0.2
production: 0
energy: 0.1
pollution: 0.1 (was 0)

Productivity Module
speed: 0
production: .05
energy: .1
pollution: .2 (was .15)

Efficiency Module
speed: 0
production: 0
energy: -0.1
pollution: .2 (was 0)

Pollution clearing
speed: 0
production: 0
energy: .05 (was 0)
pollution: -0.15

Pollution producing
speed: 0.1 (was 0)
production: 0.05 (was 0)
energy: .1 (was 0, this would be a penalty)
pollution: 0.5

Pure Speed
speed: 0.2
production: 0
energy: 0
pollution: 0.3 (was 0)

Pure Productivity
speed: 0
production: 0.05
energy: 0
pollution: 0.15 (was 0)

Green
speed: 0
production: 0
energy: -0.1
pollution: 0.05 (was -0.15, this changes a bonus into a light penalty)

It's a lot more work that you think, this kind of change basically means re-writing most of the mod's code.

Adding the settings in the first place was a huge undertaking, and they were carefully planned in such a way as to keep the minimum number of added settings (As due to the fact that you can't have your own tabs, or even categories, so everything is in one long list only broken into each mod, I want to avoid a massive wall of options) while having maximum functionality. As such, it ties many settings to each other, EG, changing the speed increase in the speed module changes it across the board for everything that has a speed increase.

As for your suggestion to add pollution to the pure modules... no, definitely not, that goes against their intended purpose. they're named pure because their down sides have been removed, they are "Pure". Since Efficiency had no down side, and neither did the Cleaning module, their effects were combined into the Green module.

I have thought about adding more possible options, or combinations of settings for the modules mod, but in the end I decided not to.
Part of the process would involve "Modularising" the coding a fair bit, EG it would change most of the huge pages of code into a few functions, including the recipe, and allow you to define an entire new set of modules with a single function with a few variables in it... Icons would have even been recolourable, allowing a few lines of code to create more than the ones I had previously pre-made.

But also decided that the benefit wouldn't be worth the effort. while it would allow you to define your own modules very easily, this would be beyond the scope of just a few settings, meaning the benefit would more be seen by people creating their own mod to create modules using the functions within mine, and would offer very little to the settings, as I would still be stuck with the original problem... to make it more customisable would require adding way more settings, bloating the settings screen, which I did not, and still do not want to do with the pretty much ZERO amount of settings customisation available.

Now, if the game allowed me to create an entire settings page just for the modules mod, I'd do it.