Hey there, I’d like to share my thoughts on that topic 
Striving for maximum efficiency
I feel like there has to be a different way to balance pipes.
As someone striving to always optimize and keeping production rates correct (building ratio) Seeing the efficiency suddenly drop makes me cringe and I have to add more buildings to keep up. I am basically trading logistics problems with space.
Logistics challenge
I personally do like the logistics challenges that I have to solve with InfraSpace. Pipes feel like cheating and give me a bad feeling about my efficiency at the same time. There is no logistics challenge with pipes, you connect the production and consumption sites and you are done. Resources more or less arrive instantly, taking away any challenge to solve.
With the game offering me no way to store anything in between (like a depot), any external gathering of water or oxygen also forces me to lay long pipelines, instead of using a mix of logistics.
Explaining the penalty ingame
There is no explanation ingame why there is a penalty. Using pipes feel more like a downgrade than an upgrade, having put all the resources into researching them. All of a sudden I have to rebalance my factories, that were perfectly balanced before.
It would be really nice to have a list of positive and negative influencers that change the efficiency on the building info panel.
Things like:
- Power (-)
- Pipes (-)
- Neighbouring buildings (+)
- etc