Both those examples are extremely arbitrary.
Increasing costs for increasing empire size is 'arbitrary'? How so?
Realistically, it is how things are -- administering/coordinating/etc. large number of cities is more complex/costly. Not including this is what's arbitrary.
The second part -- a tech to reduce said increasing costs -- is also realistic, as some forms of government are better at administering larger empires.
Still, I see no reason to replace a system that works, and fits the lore, with one that requires additional direct changes, and doesn't fit the lore.
I'm not sure what you're referring to with the 'fits/doesn't fit with the lore' bit. How does disassociating terrain from structures fit with the lore? Are are you referring to costs not increasing with empire size fitting the lore? Or...? Please to explain.
As the OP points out, cities have no relationship to terrain, other than special resources. Cities in deserts are identical to cities in lush plains which are identical to cities with thick woods. That's missing a good chance to add another layer to the game, which it sorely needs.
If this was done well it could in itself contribute to controlling city spam -- especially in a world supposedly decimated and destroyed, as lore dictates, because decimated/destroyed land would not easily support cities, making suitable city locations rare, as opposed to now where decoupling terrain from structures allows willy-nilly city placement.
The good news is, what has been asked for in this thread is insanely easy to mod into the game - in fact, there is already a "lumbermill" mod.
Heck, in early beta we could place lumberyards in woods, making city placement near woods desirable, so it was already in game and they took it out. It was a nice feature and deserved to be expanded, not removed.
