The Yale article is entirely unrealistic for residential and much of what it talks about would only work for some very large buildings that don't have any mixed usage ( if you follow the links in the article, you will find that the water system installed in the one San Fran had a starting cost of $1M dollars, which did not include all of the redundant return sanitary plumbing ).
The article glosses over the fact that you cannot re-use water in your home and that this is not going to change.
Reusing water that was used for washing your clothes?
People put all sorts of stuff into their washing machines and not all of it can be cost effectively, or even safely, reused just for toilet water.
In one word? "bleach"
Any sort of cleaning is going to involve soaps, detergents, etc... none of which you want to pump into a pipe with a smallish diameter to feed to a toilet. Environmentally? It is not worth the copper nor the electric required for a pump; a pump which would need to be designed to handle the grey water. Your municipal water is likely to be gravity fed, which is energy efficient.
Let's talk about the reality of residential properties.
Home owners are never 100% on top of every maintenance requirements and adding systems which will require ongoing maintenance and refitting? That is not viable.
Even using rainwater for toilets is not going to be cost effective, or reliable. You may believe your rain water is "all natural", but that is far from the truth once it hits your roof and makes its way to where you believe you are going to store it. It will need to be treated/cleaned before it can be use; which will then require its own pump that requires electricity.
The Yale article is misleading, at best.