I guess I don't need to mention that, but I agree with Freddy.
This system has proven to be worse than nothing. Using percentages instead of absolute numbers might solve some issues whilst introducing new ones.
The only system ensuring that players do not make connections in between cities absurdly bad, is a system that has a view on the large scale. Anything that only considers local factors will always cause anomalies here.
One system might be to remember the lengths of the initially generated intercity roads and, whenever adusting one of those, validating, that the best route in between affected cities does not become worse than the initial distance, plus maybe some percent of tolerance.
I am aware that such a system needs more detailled thoughts, will take some time to implement and is a rather low priority thing down the long list.
Don't see this as a feature request or something. It's rather a "we can do something, if we really want to", but I am not sure if it's really THAT important.
In any case, the feature as-is causes more disruption than it can solve.
It was a nice idea but it has proven to be a step to the wrong direction in practice.