The civilization capital is often place on a tile which does not maximize its potential for helping other improvements on the planet.

I feel the player should decide where to put it.   Also when a world is conquered, he should be able to swap it with another building if need be.  It is not uncommon for capitals to change after a war, think Germany after WWII or Alexandria founded by Alexander the Great or Constantinople which replaced Rome as capital of the Roman empire.

If it is too complicated to make this change, why not have a sponsorship system.  Just as planets sponsor shipyards, a civilization capital or other building could sponsor an improvement. whether or not they are adjacent or not.    Sure the bonus could be dependent on how close it is, but it would be better than an all or nothing scenario.

In this day and age where much of the Earth's consumer products are made in China even if China's client countries are not adjacent such as the U.S.   I'm not sure what's the point of having those buildings so close together.   Earth's current tech is nowhere near as advanced as those of the civilizations in the game, but we are making non-adjacent research and manufacturing facilities work together.  (The Internet helps).

If a Starbase that is in outer space can help the economics and manufacturing of a planet, then the distance between planetary improvements should not matter at all because these distances are much smaller by an order of magnitude.   It is as if the International space station could help the manufacturing capability of New York city but the city of Toronto could not.

The logistics techs should expand the area of effect an improvement has on a planet.   If a civilization is able to colonize worlds and build star bases and shipyards in outer space moving millions of people in a single ship, planetary logistics should be trivial in comparison.