Just to be clear, you can snake without a mod, manual building placement is in the options menu. You can stretch your city out quite a bit and cover huge amounts of land with your influence and connect many resources to it.
I believe troops get bonus healing in your territory, I mean I've always assumed it was the case but never really paid attention. There's currently no bonuses to anything else but that can easily be changed since the values exist in the xml, currently set to 0, you can add attack and defense multipliers to your territory if you want.
Obviously, for growth, I would want to settle on the 5/3/0 location.
Nope. 5/3/0 is terrible. You want the 4/3/2 tile, the two essence can easily double the food/growth of the city. Honestly base food and material values mean nothing for a city, essence is the only thing that matters, each point of essence is several times as valuable as a point of food or material. 1/1/4 is much, much better than 4/4/0.